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Turanli B. Decoding Systems Biology of Inflammation Signatures in Cancer Pathogenesis: Pan-Cancer Insights from 12 Common Cancers. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023; 27:483-493. [PMID: 37861711 DOI: 10.1089/omi.2023.0127] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Chronic inflammation is an important contributor to tumorigenesis in many tissues. However, the underlying mechanisms of inflammatory signaling in the tumor microenvironment are not yet fully understood in various cancers. Therefore, this study aimed to uncover the gene expression signatures of inflammation-associated proteins that lead to tumorigenesis, and with an eye to discovery of potential system biomarkers and novel drug candidates in oncology. Gene expression profiles associated with 12 common cancers (e.g., breast invasive carcinoma, colon adenocarcinoma, liver hepatocellular carcinoma, and prostate adenocarcinoma) from The Cancer Genome Atlas were retrieved and mapped to inflammation-related gene sets. Subsequently, the inflammation-associated differentially expressed genes (i-DEGs) were determined. The i-DEGs common in all cancers were proposed as tumor inflammation signatures (TIS) after pan-cancer analysis. A TIS, consisting of 45 proteins, was evaluated as a potential system biomarker based on its prognostic forecasting and secretion profiles in multiple tissues. In addition, i-DEGs for each cancer type were used as queries for drug repurposing. Narciclasine, parthenolide, and homoharringtonine were identified as potential candidates for drug repurposing. Biomarker candidates in relation to inflammation were identified such as KNG1, SPP1, and MIF. Collectively, these findings inform precision diagnostics development to distinguish individual cancer types, and can also pave the way for novel prognostic decision tools and repurposed drugs across multiple cancers. These new findings and hypotheses warrant further research toward precision/personalized medicine in oncology. Pan-cancer analysis of inflammatory mediators can open up new avenues for innovation in cancer diagnostics and therapeutics.
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Affiliation(s)
- Beste Turanli
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Türkiye
- Health Biotechnology Joint Research and Application Center of Excellence, Istanbul, Türkiye
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2
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Webber DM, Li M, MacLeod SL, Tang X, Levy JW, Karim MA, Erickson SW, Hobbs CA. Gene-Folic Acid Interactions and Risk of Conotruncal Heart Defects: Results from the National Birth Defects Prevention Study. Genes (Basel) 2023; 14:genes14010180. [PMID: 36672920 PMCID: PMC9859210 DOI: 10.3390/genes14010180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/29/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Conotruncal heart defects (CTDs) are heart malformations that affect the cardiac outflow tract and typically cause significant morbidity and mortality. Evidence from epidemiological studies suggests that maternal folate intake is associated with a reduced risk of heart defects, including CTD. However, it is unclear if folate-related gene variants and maternal folate intake have an interactive effect on the risk of CTDs. In this study, we performed targeted sequencing of folate-related genes on DNA from 436 case families with CTDs who are enrolled in the National Birth Defects Prevention Study and then tested for common and rare variants associated with CTD. We identified risk alleles in maternal MTHFS (ORmeta = 1.34; 95% CI 1.07 to 1.67), maternal NOS2 (ORmeta = 1.34; 95% CI 1.05 to 1.72), fetal MTHFS (ORmeta = 1.35; 95% CI 1.09 to 1.66), and fetal TCN2 (ORmeta = 1.38; 95% CI 1.12 to 1.70) that are associated with an increased risk of CTD among cases without folic acid supplementation. We detected putative de novo mutations in genes from the folate, homocysteine, and transsulfuration pathways and identified a significant association between rare variants in MGST1 and CTD risk. Results suggest that periconceptional folic acid supplementation is associated with decreased risk of CTD among individuals with susceptible genotypes.
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Affiliation(s)
- Daniel M. Webber
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ming Li
- Department of Epidemiology and Biostatistics, Indiana University at Bloomington, Bloomington, IN 47405, USA
| | - Stewart L. MacLeod
- Division of Birth Defects Research, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Xinyu Tang
- Biostatistics Program, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Joseph W. Levy
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48202, USA
| | - Mohammad A. Karim
- Department of Child Health, College of Medicine, University of Arizona, Phoenix, AZ 85004, USA
- Department of Neurology, Sections on Neurodevelopmental Disorders, Barrow Neurological Institute at Phoenix Children’s Hospital, Phoenix, AZ 85016, USA
| | - Stephen W. Erickson
- Center for Genomics in Public Health and Medicine, RTI International, Research Triangle Park, NC 27709, USA
| | - Charlotte A. Hobbs
- Rady Children’s Institute for Genomic Medicine, Rady Children’s Hospital, San Diego, CA 92123, USA
- Correspondence:
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Sengupta A, Naresh G, Mishra A, Parashar D, Narad P. Proteome analysis using machine learning approaches and its applications to diseases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 127:161-216. [PMID: 34340767 DOI: 10.1016/bs.apcsb.2021.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
With the tremendous developments in the fields of biological and medical technologies, huge amounts of data are generated in the form of genomic data, images in medical databases or as data on protein sequences, and so on. Analyzing this data through different tools sheds light on the particulars of the disease and our body's reactions to it, thus, aiding our understanding of the human health. Most useful of these tools is artificial intelligence and deep learning (DL). The artificially created neural networks in DL algorithms help extract viable data from the datasets, and further, to recognize patters in these complex datasets. Therefore, as a part of machine learning, DL helps us face all the various challenges that come forth during protein prediction, protein identification and their quantification. Proteomics is the study of such proteins, their structures, features, properties and so on. As a form of data science, Proteomics has helped us progress excellently in the field of genomics technologies. One of the major techniques used in proteomics studies is mass spectrometry (MS). However, MS is efficient with analysis of large datasets only with the added help of informatics approaches for data analysis and interpretation; these mainly include machine learning and deep learning algorithms. In this chapter, we will discuss in detail the applications of deep learning and various algorithms of machine learning in proteomics.
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Affiliation(s)
- Abhishek Sengupta
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - G Naresh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Astha Mishra
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Diksha Parashar
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Priyanka Narad
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India.
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Nikolaou N, Hodson L, Tomlinson JW. The role of 5-reduction in physiology and metabolic disease: evidence from cellular, pre-clinical and human studies. J Steroid Biochem Mol Biol 2021; 207:105808. [PMID: 33418075 DOI: 10.1016/j.jsbmb.2021.105808] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 12/31/2020] [Accepted: 01/03/2021] [Indexed: 01/01/2023]
Abstract
The 5-reductases (5α-reductase types 1, 2 and 3 [5αR1-3], 5β-reductase [5βR]) are steroid hormone metabolising enzymes that hold fundamental roles in human physiology and pathology. They possess broad substrate specificity converting many steroid hormones to their 5α- and 5β-reduced metabolites, as well as catalysing crucial steps in bile acid synthesis. 5αRs are fundamentally important in urogenital development by converting testosterone to the more potent androgen 5α-dihydrotestosterone (5αDHT); inactivating mutations in 5αR2 lead to disorders of sexual development. Due to the ability of the 5αRs to generate 5αDHT, they are an established drug target, and 5αR inhibitors are widely used for the treatment of androgen-dependent benign or malignant prostatic diseases. There is an emerging body of evidence to suggest that the 5-reductases can impact upon aspects of health and disease (other than urogenital development); alterations in their expression and activity have been associated with metabolic disease, polycystic ovarian syndrome, inflammation and bone metabolism. This review will outline the evidence base for the extra-urogenital role of 5-reductases from in vitro cell systems, pre-clinical models and human studies, and highlight the potential adverse effects of 5αR inhibition in human health and disease.
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Affiliation(s)
- Nikolaos Nikolaou
- Oxford Centre for Diabetes, Endocrinology and Metabolism, NIHR Oxford Biomedical Research Centre, University of Oxford, Churchill Hospital, Oxford, OX3 7LE, UK
| | - Leanne Hodson
- Oxford Centre for Diabetes, Endocrinology and Metabolism, NIHR Oxford Biomedical Research Centre, University of Oxford, Churchill Hospital, Oxford, OX3 7LE, UK
| | - Jeremy W Tomlinson
- Oxford Centre for Diabetes, Endocrinology and Metabolism, NIHR Oxford Biomedical Research Centre, University of Oxford, Churchill Hospital, Oxford, OX3 7LE, UK.
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Proteomics and Metabolomics Approaches towards a Functional Insight onto AUTISM Spectrum Disorders: Phenotype Stratification and Biomarker Discovery. Int J Mol Sci 2020; 21:ijms21176274. [PMID: 32872562 PMCID: PMC7504551 DOI: 10.3390/ijms21176274] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 08/25/2020] [Accepted: 08/27/2020] [Indexed: 12/19/2022] Open
Abstract
Autism spectrum disorders (ASDs) are neurodevelopmental disorders characterized by behavioral alterations and currently affect about 1% of children. Significant genetic factors and mechanisms underline the causation of ASD. Indeed, many affected individuals are diagnosed with chromosomal abnormalities, submicroscopic deletions or duplications, single-gene disorders or variants. However, a range of metabolic abnormalities has been highlighted in many patients, by identifying biofluid metabolome and proteome profiles potentially usable as ASD biomarkers. Indeed, next-generation sequencing and other omics platforms, including proteomics and metabolomics, have uncovered early age disease biomarkers which may lead to novel diagnostic tools and treatment targets that may vary from patient to patient depending on the specific genomic and other omics findings. The progressive identification of new proteins and metabolites acting as biomarker candidates, combined with patient genetic and clinical data and environmental factors, including microbiota, would bring us towards advanced clinical decision support systems (CDSSs) assisted by machine learning models for advanced ASD-personalized medicine. Herein, we will discuss novel computational solutions to evaluate new proteome and metabolome ASD biomarker candidates, in terms of their recurrence in the reviewed literature and laboratory medicine feasibility. Moreover, the way to exploit CDSS, performed by artificial intelligence, is presented as an effective tool to integrate omics data to electronic health/medical records (EHR/EMR), hopefully acting as added value in the near future for the clinical management of ASD.
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Cerrato A, Capriotti AL, Capuano F, Cavaliere C, Montone AMI, Montone CM, Piovesana S, Zenezini Chiozzi R, Laganà A. Identification and Antimicrobial Activity of Medium-Sized and Short Peptides from Yellowfin Tuna ( Thunnus albacares) Simulated Gastrointestinal Digestion. Foods 2020; 9:foods9091185. [PMID: 32867059 PMCID: PMC7555217 DOI: 10.3390/foods9091185] [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: 07/27/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 12/13/2022] Open
Abstract
Due to the rapidly increasing resistance to conventional antibiotics, antimicrobial peptides are emerging as promising novel drug candidates. In this study, peptide fragments were obtained from yellowfin tuna muscle by simulated gastrointestinal digestion, and their antimicrobial activity towards Gram-positive and Gram-negative bacteria was investigated. In particular, the antimicrobial activity of both medium- and short-sized peptides was investigated by using two dedicated approaches. Medium-sized peptides were purified by solid phase extraction on C18, while short peptides were purified thanks to a graphitized carbon black sorbent. For medium-sized peptide characterization, a peptidomic strategy based on shotgun proteomics analysis was employed, and identification was achieved by matching protein sequence database by homology, as yellowfin tuna is a non-model organism, leading to the identification of 403 peptides. As for short peptide sequences, an untargeted suspect screening approach was carried out by means of an inclusion list presenting the exact mass to charge ratios (m/z) values for all di-, tri- and tetrapeptides. In total, 572 short sequences were identified thanks to a customized workflow dedicated to short peptide analysis implemented on Compound Discoverer software.
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Affiliation(s)
- Andrea Cerrato
- Department of Chemistry, Università di Roma “La Sapienza”, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.C.); (A.L.C.); (C.C.); (S.P.); (A.L.)
| | - Anna Laura Capriotti
- Department of Chemistry, Università di Roma “La Sapienza”, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.C.); (A.L.C.); (C.C.); (S.P.); (A.L.)
| | - Federico Capuano
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute 2, 80055 Portici (NA), Italy; (F.C.); (A.M.I.M.)
| | - Chiara Cavaliere
- Department of Chemistry, Università di Roma “La Sapienza”, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.C.); (A.L.C.); (C.C.); (S.P.); (A.L.)
| | - Angela Michela Immacolata Montone
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute 2, 80055 Portici (NA), Italy; (F.C.); (A.M.I.M.)
- Department of Industrial Engineering, Università degli Studi di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy
| | - Carmela Maria Montone
- Department of Chemistry, Università di Roma “La Sapienza”, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.C.); (A.L.C.); (C.C.); (S.P.); (A.L.)
- Correspondence: ; Tel.: +39-06-4991-3062
| | - Susy Piovesana
- Department of Chemistry, Università di Roma “La Sapienza”, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.C.); (A.L.C.); (C.C.); (S.P.); (A.L.)
| | - Riccardo Zenezini Chiozzi
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands;
| | - Aldo Laganà
- Department of Chemistry, Università di Roma “La Sapienza”, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.C.); (A.L.C.); (C.C.); (S.P.); (A.L.)
- CNR NANOTEC, Campus Ecotekne, University of Salento, Via Monteroni, 73100 Lecce, Italy
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Tanigawa Y, Wainberg M, Karjalainen J, Kiiskinen T, Venkataraman G, Lemmelä S, Turunen JA, Graham RR, Havulinna AS, Perola M, Palotie A, Daly MJ, Rivas MA. Rare protein-altering variants in ANGPTL7 lower intraocular pressure and protect against glaucoma. PLoS Genet 2020; 16:e1008682. [PMID: 32369491 PMCID: PMC7199928 DOI: 10.1371/journal.pgen.1008682] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 02/18/2020] [Indexed: 12/17/2022] Open
Abstract
Protein-altering variants that are protective against human disease provide in vivo validation of therapeutic targets. Here we use genotyping data from UK Biobank (n = 337,151 unrelated White British individuals) and FinnGen (n = 176,899) to conduct a search for protein-altering variants conferring lower intraocular pressure (IOP) and protection against glaucoma. Through rare protein-altering variant association analysis, we find a missense variant in ANGPTL7 in UK Biobank (rs28991009, p.Gln175His, MAF = 0.8%, genotyped in 82,253 individuals with measured IOP and an independent set of 4,238 glaucoma patients and 250,660 controls) that significantly lowers IOP (β = -0.53 and -0.67 mmHg for heterozygotes, -3.40 and -2.37 mmHg for homozygotes, P = 5.96 x 10-9 and 1.07 x 10-13 for corneal compensated and Goldman-correlated IOP, respectively) and is associated with 34% reduced risk of glaucoma (P = 0.0062). In FinnGen, we identify an ANGPTL7 missense variant at a greater than 50-fold increased frequency in Finland compared with other populations (rs147660927, p.Arg220Cys, MAF Finland = 4.3%), which was genotyped in 6,537 glaucoma patients and 170,362 controls and is associated with a 29% lower glaucoma risk (P = 1.9 x 10-12 for all glaucoma types and also protection against its subtypes including exfoliation, primary open-angle, and primary angle-closure). We further find three rarer variants in UK Biobank, including a protein-truncating variant, which confer a strong composite lowering of IOP (P = 0.0012 and 0.24 for Goldman-correlated and corneal compensated IOP, respectively), suggesting the protective mechanism likely resides in the loss of interaction or function. Our results support inhibition or down-regulation of ANGPTL7 as a therapeutic strategy for glaucoma.
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Affiliation(s)
- Yosuke Tanigawa
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, California, United States of America
| | - Michael Wainberg
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, California, United States of America
| | - Juha Karjalainen
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Tuomo Kiiskinen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Guhan Venkataraman
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, California, United States of America
| | - Susanna Lemmelä
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Joni A. Turunen
- Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Folkhälsan Research Center, Biomedicum Helsinki, Helsinki, Finland
| | - Robert R. Graham
- Maze Therapeutics, South San Francisco, California, United States of America
| | - Aki S. Havulinna
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Markus Perola
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Aarno Palotie
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | | | - Mark J. Daly
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Manuel A. Rivas
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, California, United States of America
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Plant D, Barton A. Adding value to real-world data: the role of biomarkers. Rheumatology (Oxford) 2020; 59:31-38. [PMID: 31329972 PMCID: PMC6909909 DOI: 10.1093/rheumatology/kez113] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 02/28/2019] [Indexed: 12/13/2022] Open
Abstract
Adding biomarker information to real world datasets (e.g. biomarker data collected into disease/drug registries) can enhance mechanistic understanding of intra-patient differences in disease trajectories and differences in important clinical outcomes. Biomarkers can detect pathologies present early in disease potentially paving the way for preventative intervention strategies, which may help patients to avoid disability, poor treatment outcome, disease sequelae and premature mortality. However, adding biomarker data to real world datasets comes with a number of important challenges including sample collection and storage, study design and data analysis and interpretation. In this narrative review we will consider the benefits and challenges of adding biomarker data to real world datasets and discuss how biomarker data have added to our understanding of complex diseases, focusing on rheumatoid arthritis.
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Affiliation(s)
- Darren Plant
- Manchester Academic Health Science Centre, The University of Manchester, Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, UK.,Manchester Academic Health Science Centre, NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Anne Barton
- Manchester Academic Health Science Centre, The University of Manchester, Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, UK.,Manchester Academic Health Science Centre, NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester, UK
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Kao RL, Truscott LC, Chiou TT, Tsai W, Wu AM, De Oliveira SN. A Cetuximab-Mediated Suicide System in Chimeric Antigen Receptor-Modified Hematopoietic Stem Cells for Cancer Therapy. Hum Gene Ther 2020; 30:413-428. [PMID: 30860401 DOI: 10.1089/hum.2018.180] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Using gene modification of hematopoietic stem cells (HSC) to create persistent generation of multilineage immune effectors to target cancer cells directly is proposed. Gene-modified human HSC have been used to introduce genes to correct, prevent, or treat diseases. Concerns regarding malignant transformation, abnormal hematopoiesis, and autoimmunity exist, making the co-delivery of a suicide gene a necessary safety measure. Truncated epidermal growth factor receptor (EGFRt) was tested as a suicide gene system co-delivered with anti-CD19 chimeric antigen receptor (CAR) to human HSC. Third-generation self-inactivating lentiviral vectors were used to co-deliver an anti-CD19 CAR and EGFRt. In vitro, gene-modified HSC were differentiated into myeloid cells to allow transgene expression. An antibody-dependent cell-mediated cytotoxicity (ADCC) assay was used, incubating target cells with leukocytes and monoclonal antibody cetuximab to determine the percentage of surviving cells. In vivo, gene-modified HSC were engrafted into NSG mice with subsequent treatment with intraperitoneal cetuximab. Persistence of gene-modified cells was assessed by flow cytometry, droplet digital polymerase chain reaction (ddPCR), and positron emission tomography (PET) imaging using 89Zr-Cetuximab. Cytotoxicity was significantly increased (p = 0.01) in target cells expressing EGFRt after incubation with leukocytes and cetuximab 1 μg/mL compared to EGFRt+ cells without cetuximab and non-transduced cells with or without cetuximab, at all effector:target ratios. Mice humanized with gene-modified HSC presented significant ablation of gene-modified cells after treatment (p = 0.002). Remaining gene-modified cells were close to background on flow cytometry and within two logs of decrease of vector copy numbers by ddPCR in mouse tissues. PET imaging confirmed ablation with a decrease of an average of 82.5% after cetuximab treatment. These results give proof of principle for CAR-modified HSC regulated by a suicide gene. Further studies are needed to enable clinical translation. Cetuximab ADCC of EGFRt-modified cells caused effective killing. Different ablation approaches, such as inducible caspase 9 or co-delivery of other inert cell markers, should also be evaluated.
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Affiliation(s)
- Roy L Kao
- 1 Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Laurel C Truscott
- 1 Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Tzu-Ting Chiou
- 1 Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Wenting Tsai
- 2 Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, California
| | - Anna M Wu
- 2 Department of Molecular and Medical Pharmacology, UCLA, Los Angeles, California
| | - Satiro N De Oliveira
- 1 Department of Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, California
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Artiukhov AV, Grabarska A, Gumbarewicz E, Aleshin VA, Kähne T, Obata T, Kazantsev AV, Lukashev NV, Stepulak A, Fernie AR, Bunik VI. Synthetic analogues of 2-oxo acids discriminate metabolic contribution of the 2-oxoglutarate and 2-oxoadipate dehydrogenases in mammalian cells and tissues. Sci Rep 2020; 10:1886. [PMID: 32024885 PMCID: PMC7002488 DOI: 10.1038/s41598-020-58701-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 01/03/2020] [Indexed: 02/06/2023] Open
Abstract
The biological significance of the DHTKD1-encoded 2-oxoadipate dehydrogenase (OADH) remains obscure due to its catalytic redundancy with the ubiquitous OGDH-encoded 2-oxoglutarate dehydrogenase (OGDH). In this work, metabolic contributions of OADH and OGDH are discriminated by exposure of cells/tissues with different DHTKD1 expression to the synthesized phosphonate analogues of homologous 2-oxodicarboxylates. The saccharopine pathway intermediates and phosphorylated sugars are abundant when cellular expressions of DHTKD1 and OGDH are comparable, while nicotinate and non-phosphorylated sugars are when DHTKD1 expression is order(s) of magnitude lower than that of OGDH. Using succinyl, glutaryl and adipoyl phosphonates on the enzyme preparations from tissues with varied DHTKD1 expression reveals the contributions of OADH and OGDH to oxidation of 2-oxoadipate and 2-oxoglutarate in vitro. In the phosphonates-treated cells with the high and low DHTKD1 expression, adipate or glutarate, correspondingly, are the most affected metabolites. The marker of fatty acid β-oxidation, adipate, is mostly decreased by the shorter, OGDH-preferring, phosphonate, in agreement with the known OGDH dependence of β-oxidation. The longest, OADH-preferring, phosphonate mostly affects the glutarate level. Coupled decreases in sugars and nicotinate upon the OADH inhibition link the perturbation in glucose homeostasis, known in OADH mutants, to the nicotinate-dependent NAD metabolism.
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Affiliation(s)
- Artem V Artiukhov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Aneta Grabarska
- Department of Biochemistry and Molecular Biology of Medical University of Lublin, Lublin, Poland
| | - Ewelina Gumbarewicz
- Department of Biochemistry and Molecular Biology of Medical University of Lublin, Lublin, Poland
| | - Vasily A Aleshin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Thilo Kähne
- Institute of Experimental Internal Medicine, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Toshihiro Obata
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Department of Biochemistry, George W. Beadle Center, University of Nebraska-Lincoln, Lincoln, NE, 68588-0664, USA
| | | | | | - Andrzej Stepulak
- Department of Biochemistry and Molecular Biology of Medical University of Lublin, Lublin, Poland
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Victoria I Bunik
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
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11
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Nanda H, Ponnusamy N, Odumpatta R, Jeyakanthan J, Mohanapriya A. Exploring genetic targets of psoriasis using genome wide association studies (GWAS) for drug repurposing. 3 Biotech 2020; 10:43. [PMID: 31988837 PMCID: PMC6954159 DOI: 10.1007/s13205-019-2038-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 12/23/2019] [Indexed: 12/26/2022] Open
Abstract
Psoriasis is a chronic inflammatory disease causing itching in the body and pain in the joints. Currently, no permanent cure is available at a commercial level for this disease. Genome wide association studies (GWAS) provide a deeper insight that helps in better understanding this disease and further possible cure of this disease. The major goal of the present study is to identify potent genetic targets of psoriasis disease using GWAS approach and identify drugs for repurposing. The methods used include GWAS catalogue, GeneAnalytics, canSAR protein annotation tool, VarElect, Drug bank, Proteomics database, ProTox software. By exploring GWAS catalogue, 126 psoriasis associated genes (PAG) were identified. 68 genes found to be druggable were obtained from canSAR protein annotation tool. Localization results depict that maximum genes are present in cytoplasmic cellular components. The superpathways obtained from GeneAnalytics resulted in involvement of these genes in the immune system, Jak/Stat pathway, Th17 and Wnt pathways. Two genes Interleukin 13 (IL13) and POLI are Food and Drug Administration (FDA) approved targets. Small compounds for these targets were analysed for drug-likeliness, toxicity and mutagenecity properties. The FDA approved drug pandel was found to possess desirable properties. The medications used for psoriasis causes mild to severe side effects and does not work well always. Hence we propose drug repurposing strategy to use existing drugs for new therapies. Therefore, the drug pandel could be explored further and repurposed to treat psoriasis.
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Affiliation(s)
- Harshit Nanda
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014 India
| | - Nirmaladevi Ponnusamy
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014 India
| | - Rajasree Odumpatta
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014 India
| | - Jeyaraman Jeyakanthan
- Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu 630004 India
| | - Arumugam Mohanapriya
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014 India
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12
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Nemtsova MV, Zaletaev DV, Bure IV, Mikhaylenko DS, Kuznetsova EB, Alekseeva EA, Beloukhova MI, Deviatkin AA, Lukashev AN, Zamyatnin AA. Epigenetic Changes in the Pathogenesis of Rheumatoid Arthritis. Front Genet 2019; 10:570. [PMID: 31258550 PMCID: PMC6587113 DOI: 10.3389/fgene.2019.00570] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 05/31/2019] [Indexed: 01/06/2023] Open
Abstract
Rheumatoid arthritis (RA) is a systemic autoimmune disease that affects about 1% of the world’s population. The etiology of RA remains unknown. It is considered to occur in the presence of genetic and environmental factors. An increasing body of evidence pinpoints that epigenetic modifications play an important role in the regulation of RA pathogenesis. Epigenetics causes heritable phenotype changes that are not determined by changes in the DNA sequence. The major epigenetic mechanisms include DNA methylation, histone proteins modifications and changes in gene expression caused by microRNAs and other non-coding RNAs. These modifications are reversible and could be modulated by diet, drugs, and other environmental factors. Specific changes in DNA methylation, histone modifications and abnormal expression of non-coding RNAs associated with RA have already been identified. This review focuses on the role of these multiple epigenetic factors in the pathogenesis and progression of the disease, not only in synovial fibroblasts, immune cells, but also in the peripheral blood of patients with RA, which clearly shows their high diagnostic potential and promising targets for therapy in the future.
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Affiliation(s)
- Marina V Nemtsova
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
| | - Dmitry V Zaletaev
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
| | - Irina V Bure
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Dmitry S Mikhaylenko
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
| | - Ekaterina B Kuznetsova
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
| | - Ekaterina A Alekseeva
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russia
| | - Marina I Beloukhova
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Andrei A Deviatkin
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Alexander N Lukashev
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Andrey A Zamyatnin
- Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia.,A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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13
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Duarte Y, Márquez-Miranda V, Miossec MJ, González-Nilo F. Integration of target discovery, drug discovery and drug delivery: A review on computational strategies. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2019; 11:e1554. [PMID: 30932351 DOI: 10.1002/wnan.1554] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 12/14/2018] [Accepted: 01/23/2019] [Indexed: 12/22/2022]
Abstract
Most of the computational tools involved in drug discovery developed during the 1980s were largely based on computational chemistry, quantitative structure-activity relationship (QSAR) and cheminformatics. Subsequently, the advent of genomics in the 2000s gave rise to a huge number of databases and computational tools developed to analyze large quantities of data, through bioinformatics, to obtain valuable information about the genomic regulation of different organisms. Target identification and validation is a long process during which evidence for and against a target is accumulated in the pursuit of developing new drugs. Finally, the drug delivery system appears as a novel approach to improve drug targeting and releasing into the cells, leading to new opportunities to improve drug efficiency and avoid potential secondary effects. In each area: target discovery, drug discovery and drug delivery, different computational strategies are being developed to accelerate the process of selection and discovery of new tools to be applied to different scientific fields. Research on these three topics is growing rapidly, but still requires a global view of this landscape to detect the most challenging bottleneck and how computational tools could be integrated in each topic. This review describes the current state of the art in computational strategies for target discovery, drug discovery and drug delivery and how these fields could be integrated. Finally, we will discuss about the current needs in these fields and how the continuous development of databases and computational tools will impact on the improvement of those areas. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Therapeutic Approaches and Drug Discovery > Nanomedicine for Infectious Disease Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.
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Affiliation(s)
- Yorley Duarte
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Valeria Márquez-Miranda
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Matthieu J Miossec
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Fernando González-Nilo
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.,Centro Interdisciplinario de Neurociencias de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
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14
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Moutal A, Kalinin S, Kowal K, Marangoni N, Dupree J, Lin SX, Lis K, Lisi L, Hensley K, Khanna R, Feinstein DL. Neuronal Conditional Knockout of Collapsin Response Mediator Protein 2 Ameliorates Disease Severity in a Mouse Model of Multiple Sclerosis. ASN Neuro 2019; 11:1759091419892090. [PMID: 31795726 PMCID: PMC6893573 DOI: 10.1177/1759091419892090] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 10/23/2019] [Accepted: 11/02/2019] [Indexed: 01/17/2023] Open
Abstract
We previously showed that treatment with lanthionine ketimine ethyl ester (LKE) reduced disease severity and axonal damage in an experimental autoimmune encephalomyelitis (EAE) mouse model of multiple sclerosis and increased neuronal maturation and survival in vitro . A major target of LKE is collapsin response mediator protein 2 (CRMP2), suggesting this protein may mediate LKE actions. We now show that conditional knockout of CRMP2 from neurons using a CamK2a promoter to drive Cre recombinase expression reduces disease severity in the myelin oligodendrocyte glycoprotein (MOG)35–55 EAE model, associated with decreased spinal cord axonal damage, and less glial activation in the cerebellum, but not the spinal cord. Immunohistochemical staining and quantitative polymerase chain reaction show CRMP2 depletion from descending motor neurons in the motor cortex, but not from spinal cord neurons, suggesting that the benefits of CRMP2 depletion on EAE may stem from effects on upper motor neurons. In addition, mice in which CRMP2 S522 phosphorylation was prevented by substitution for an alanine residue also showed reduced EAE severity. These results show that modification of CRMP2 expression and phosphorylation can influence the course of EAE and suggests that treatment with CRMP2 modulators such as LKE act in part by reducing CRMP2 S522 phosphorylation.
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Affiliation(s)
| | | | | | | | | | | | - Kinga Lis
- University of Illinois, Chicago, IL, USA
| | - Lucia Lisi
- Universita Cattolica del Sacro Cuore, Rome,
Italy
| | - Kenneth Hensley
- Arkansas College of Osteopathic Medicine, Fort Smith,
AR, USA
| | | | - Douglas L. Feinstein
- University of Illinois, Chicago, IL, USA
- Jesse Brown VA Medical Center, Chicago, IL, USA
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15
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Context-dependent prediction of protein complexes by SiComPre. NPJ Syst Biol Appl 2018; 4:37. [PMID: 30245847 PMCID: PMC6141528 DOI: 10.1038/s41540-018-0073-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 08/21/2018] [Accepted: 08/29/2018] [Indexed: 11/09/2022] Open
Abstract
Most cellular processes are regulated by groups of proteins interacting together to form protein complexes. Protein compositions vary between different tissues or disease conditions enabling or preventing certain protein-protein interactions and resulting in variations in the complexome. Quantitative and qualitative characterization of context-specific protein complexes will help to better understand context-dependent variations in the physiological behavior of cells. Here, we present SiComPre 1.0, a computational tool that predicts context-specific protein complexes by integrating multi-omics sources. SiComPre outperforms other protein complex prediction tools in qualitative predictions and is unique in giving quantitative predictions on the complexome depending on the specific interactions and protein abundances defined by the user. We provide tutorials and examples on the complexome prediction of common model organisms, various human tissues and how the complexome is affected by drug treatment.
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16
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Predicting the evolution of Escherichia coli by a data-driven approach. Nat Commun 2018; 9:3562. [PMID: 30177705 PMCID: PMC6120903 DOI: 10.1038/s41467-018-05807-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 06/12/2018] [Indexed: 12/31/2022] Open
Abstract
A tantalizing question in evolutionary biology is whether evolution can be predicted from past experiences. To address this question, we created a coherent compendium of more than 15,000 mutation events for the bacterium Escherichia coli under 178 distinct environmental settings. Compendium analysis provides a comprehensive view of the explored environments, mutation hotspots and mutation co-occurrence. While the mutations shared across all replicates decrease with the number of replicates, our results argue that the pairwise overlapping ratio remains the same, regardless of the number of replicates. An ensemble of predictors trained on the mutation compendium and tested in forward validation over 35 evolution replicates achieves a 49.2 ± 5.8% (mean ± std) precision and 34.5 ± 5.7% recall in predicting mutation targets. This work demonstrates how integrated datasets can be harnessed to create predictive models of evolution at a gene level and elucidate the effect of evolutionary processes in well-defined environments. How reproducible evolutionary processes are remains an important question in evolutionary biology. Here, the authors compile a compendium of more than 15,000 mutation events for Escherichia coli under 178 distinct environmental settings, and develop an ensemble of predictors to predict evolution at a gene level.
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17
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Kim J, Bamlet WR, Oberg AL, Chaffee KG, Donahue G, Cao XJ, Chari S, Garcia BA, Petersen GM, Zaret KS. Detection of early pancreatic ductal adenocarcinoma with thrombospondin-2 and CA19-9 blood markers. Sci Transl Med 2018; 9:9/398/eaah5583. [PMID: 28701476 DOI: 10.1126/scitranslmed.aah5583] [Citation(s) in RCA: 160] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 12/16/2016] [Accepted: 04/27/2017] [Indexed: 12/15/2022]
Abstract
Markers are needed to facilitate early detection of pancreatic ductal adenocarcinoma (PDAC), which is often diagnosed too late for effective therapy. Starting with a PDAC cell reprogramming model that recapitulated the progression of human PDAC, we identified secreted proteins and tested a subset as potential markers of PDAC. We optimized an enzyme-linked immunosorbent assay (ELISA) using plasma samples from patients with various stages of PDAC, from individuals with benign pancreatic disease, and from healthy controls. A phase 1 discovery study (n = 20), a phase 2a validation study (n = 189), and a second phase 2b validation study (n = 537) revealed that concentrations of plasma thrombospondin-2 (THBS2) discriminated among all stages of PDAC consistently. The receiver operating characteristic (ROC) c-statistic was 0.76 in the phase 1 study, 0.84 in the phase 2a study, and 0.87 in the phase 2b study. The plasma concentration of THBS2 was able to discriminate resectable stage I cancer as readily as stage III/IV PDAC tumors. THBS2 plasma concentrations combined with those for CA19-9, a previously identified PDAC marker, yielded a c-statistic of 0.96 in the phase 2a study and 0.97 in the phase 2b study. THBS2 data improved the ability of CA19-9 to distinguish PDAC from pancreatitis. With a specificity of 98%, the combination of THBS2 and CA19-9 yielded a sensitivity of 87% for PDAC in the phase 2b study. A THBS2 and CA19-9 blood marker panel measured with a conventional ELISA may improve the detection of patients at high risk for PDAC.
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Affiliation(s)
- Jungsun Kim
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Abramson Cancer Center (Tumor Biology Program), Perelman School of Medicine, University of Pennsylvania, 9-131 Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5157, USA
| | - William R Bamlet
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Ann L Oberg
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Kari G Chaffee
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Greg Donahue
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Abramson Cancer Center (Tumor Biology Program), Perelman School of Medicine, University of Pennsylvania, 9-131 Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5157, USA
| | - Xing-Jun Cao
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Suresh Chari
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Benjamin A Garcia
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gloria M Petersen
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Abramson Cancer Center (Tumor Biology Program), Perelman School of Medicine, University of Pennsylvania, 9-131 Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104-5157, USA.
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18
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Dhungel B, Andrzejewski S, Jayachandran A, Shrestha R, Ramlogan-Steel CA, Layton CJ, Steel JC. Evaluation of the Glypican 3 promoter for transcriptional targeting of hepatocellular carcinoma. Gene Ther 2018; 25:115-128. [DOI: 10.1038/s41434-018-0002-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 12/01/2017] [Accepted: 12/27/2017] [Indexed: 12/19/2022]
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19
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Abstract
Cellular functions are often performed by multiprotein structures called protein complexes. These complexes are dynamic structures that evolve during the cell cycle or in response to external and internal stimuli, and are tightly regulated by protein expression in different tissues resulting in quantitative and qualitative variation of protein complexes. Advances in high-throughput techniques, such as mass-spectrometry and yeast two-hybrid provided a large amount of data on protein-protein interactions. This sparked the development of computational methods able to predict protein complex formation under a variety of biological and clinical conditions. However, the challenges that need to be addressed for successful computational protein complex prediction are highly complex.The post-genomic era saw an emerging number of algorithms and software, which are able to predict protein complexes from protein-protein interaction networks and a variety of other sources. Despite the high capacity of these methods to qualitatively predict protein complexes, they could provide only limited or no quantitative information of the predicted complexes. Recently, a new large-scale simulation of protein complexes was able to achieve this task by simulating protein complex formation on the proteome scale.In this chapter, we review representative methods that can predict multiple protein complexes at different scales and discuss how these can be combined with emerging sources of data in order to improve protein complex characterization.
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20
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Morrell WC, Birkel GW, Forrer M, Lopez T, Backman TWH, Dussault M, Petzold CJ, Baidoo EEK, Costello Z, Ando D, Alonso-Gutierrez J, George KW, Mukhopadhyay A, Vaino I, Keasling JD, Adams PD, Hillson NJ, Garcia Martin H. The Experiment Data Depot: A Web-Based Software Tool for Biological Experimental Data Storage, Sharing, and Visualization. ACS Synth Biol 2017; 6:2248-2259. [PMID: 28826210 DOI: 10.1021/acssynbio.7b00204] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Although recent advances in synthetic biology allow us to produce biological designs more efficiently than ever, our ability to predict the end result of these designs is still nascent. Predictive models require large amounts of high-quality data to be parametrized and tested, which are not generally available. Here, we present the Experiment Data Depot (EDD), an online tool designed as a repository of experimental data and metadata. EDD provides a convenient way to upload a variety of data types, visualize these data, and export them in a standardized fashion for use with predictive algorithms. In this paper, we describe EDD and showcase its utility for three different use cases: storage of characterized synthetic biology parts, leveraging proteomics data to improve biofuel yield, and the use of extracellular metabolite concentrations to predict intracellular metabolic fluxes.
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Affiliation(s)
- William C. Morrell
- DOE Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biotechnology
and Bioengineering and Biomass Science and Conversion Department, Sandia National Laboratories, Livermore, California 94550, United States
| | - Garrett W. Birkel
- DOE Joint BioEnergy Institute, Emeryville, California 94608, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Mark Forrer
- DOE Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biotechnology
and Bioengineering and Biomass Science and Conversion Department, Sandia National Laboratories, Livermore, California 94550, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
| | - Teresa Lopez
- DOE Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biotechnology
and Bioengineering and Biomass Science and Conversion Department, Sandia National Laboratories, Livermore, California 94550, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
| | - Tyler W. H. Backman
- DOE Joint BioEnergy Institute, Emeryville, California 94608, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Michael Dussault
- DOE Joint BioEnergy Institute, Emeryville, California 94608, United States
| | - Christopher J. Petzold
- DOE Joint BioEnergy Institute, Emeryville, California 94608, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Edward E. K. Baidoo
- DOE Joint BioEnergy Institute, Emeryville, California 94608, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Zak Costello
- DOE Joint BioEnergy Institute, Emeryville, California 94608, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - David Ando
- DOE Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jorge Alonso-Gutierrez
- DOE Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Kevin W. George
- DOE Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Aindrila Mukhopadhyay
- DOE Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Ian Vaino
- DOE Joint BioEnergy Institute, Emeryville, California 94608, United States
| | - Jay D. Keasling
- DOE Joint BioEnergy Institute, Emeryville, California 94608, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- Department
of Bioengineering, University of California, Berkeley, California 94720, United States
| | - Paul D. Adams
- DOE Joint BioEnergy Institute, Emeryville, California 94608, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Nathan J. Hillson
- DOE Joint BioEnergy Institute, Emeryville, California 94608, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DNA
Synthesis Science Program, DOE Joint Genome Institute, Walnut Creek, California 94598, United States
| | - Hector Garcia Martin
- DOE Joint BioEnergy Institute, Emeryville, California 94608, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- BCAM, Basque Center for Applied Mathematics, 48009 Bilbao, Spain
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21
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Kolker E, Özdemir V, Kolker E. How Healthcare Can Refocus on Its Super-Customers (Patients, n =1) and Customers (Doctors and Nurses) by Leveraging Lessons from Amazon, Uber, and Watson. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2017; 20:329-33. [PMID: 27310474 DOI: 10.1089/omi.2016.0077] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Healthcare is transforming with data-intensive omics technologies and Big Data. The "revolution" has already happened in technology, but the bottlenecks have shifted to the social domain: Who can be empowered by Big Data? Who are the users and customers? In this review and innovation field analysis, we introduce the idea of a "super-customer" versus "customer" and relate both to 21st century healthcare. A "super-customer" in healthcare is the patient, sample size of n = 1, while "customers" are the providers of healthcare (e.g., doctors and nurses). The super-customers have been patients, enabled by unprecedented social practices, such as the ability to track one's physical activities, personal genomics, patient advocacy for greater autonomy, and self-governance, to name but a few. In contrast, the originally intended customers-providers, doctors, and nurses-have relatively lagged behind. With patients as super-customers, there are valuable lessons to be learned from industry examples, such as Amazon and Uber. To offer superior quality service, healthcare organizations have to refocus on the needs, pains, and aspirations of their super-customers by enabling the customers. We propose a strategic solution to this end: the PPT-DAM (People-Process-Technology empowered by Data, Analytics, and Metrics) approach. When applied together with the classic Experiment-Execute-Evaluate iterative methodology, we suggest PPT-DAM is an extremely powerful approach to deliver quality health services to super-customers and customers. As an example, we describe the PPT-DAM implementation by the Benchmarking Improvement Program at the Seattle Children's Hospital. Finally, we forecast that cognitive systems in general and IBM Watson in particular, if properly implemented, can bring transformative and sustainable capabilities in healthcare far beyond the current ones.
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Affiliation(s)
| | - Vural Özdemir
- 2 Faculty of Communications and the Office of the President, International Technology and Innovation Policy, Gaziantep University , Gaziantep, Turkey .,3 Target Technology Transfer Office (TTO) , Gaziantep Technopark, Gaziantep, Turkey .,4 Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham (Amrita University) , Kerala, India .,5 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington
| | - Eugene Kolker
- 5 Data-Enabled Life Sciences Alliance (DELSA Global) , Seattle, Washington.,6 CDO Analytics, Seattle Children's Hospital (SCH) , Seattle, Washington.,7 Department of Biomedical Informatics and Medical Education, University of Washington , Seattle, Washington.,8 Department of Pediatrics, School of Medicine, University of Washington , Seattle, Washington.,9 Department of Chemistry and Chemical Biology, College of Science, Northeastern University , Boston, Massachusetts
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22
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Raphael I, Webb J, Gomez-Rivera F, Chase Huizar CA, Gupta R, Arulanandam BP, Wang Y, Haskins WE, Forsthuber TG. Serum Neuroinflammatory Disease-Induced Central Nervous System Proteins Predict Clinical Onset of Experimental Autoimmune Encephalomyelitis. Front Immunol 2017; 8:812. [PMID: 28769926 PMCID: PMC5512177 DOI: 10.3389/fimmu.2017.00812] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/27/2017] [Indexed: 11/24/2022] Open
Abstract
There is an urgent need in multiple sclerosis (MS) patients to develop biomarkers and laboratory tests to improve early diagnosis, predict clinical relapses, and optimize treatment responses. In healthy individuals, the transport of proteins across the blood–brain barrier (BBB) is tightly regulated, whereas, in MS, central nervous system (CNS) inflammation results in damage to neuronal tissues, disruption of BBB integrity, and potential release of neuroinflammatory disease-induced CNS proteins (NDICPs) into CSF and serum. Therefore, changes in serum NDICP abundance could serve as biomarkers of MS. Here, we sought to determine if changes in serum NDICPs are detectable prior to clinical onset of experimental autoimmune encephalomyelitis (EAE) and, therefore, enable prediction of disease onset. Importantly, we show in longitudinal serum specimens from individual mice with EAE that pre-onset expression waves of synapsin-2, glutamine synthetase, enolase-2, and synaptotagmin-1 enable the prediction of clinical disease with high sensitivity and specificity. Moreover, we observed differences in serum NDICPs between active and passive immunization in EAE, suggesting hitherto not appreciated differences for disease induction mechanisms. Our studies provide the first evidence for enabling the prediction of clinical disease using serum NDICPs. The results provide proof-of-concept for the development of high-confidence serum NDICP expression waves and protein biomarker candidates for MS.
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Affiliation(s)
- Itay Raphael
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, United States.,Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Johanna Webb
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, United States
| | - Francisco Gomez-Rivera
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, United States
| | - Carol A Chase Huizar
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, United States
| | - Rishein Gupta
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, United States
| | - Bernard P Arulanandam
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, United States
| | - Yufeng Wang
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, United States
| | - William E Haskins
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, United States
| | - Thomas G Forsthuber
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, United States
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23
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Jin F, Wang Y, Wang X, Wu Y, Wang X, Liu Q, Zhu Y, Liu E, Fan J, Wang Y. Bre Enhances Osteoblastic Differentiation by Promoting the Mdm2-Mediated Degradation of p53. Stem Cells 2017; 35:1760-1772. [PMID: 28436570 DOI: 10.1002/stem.2620] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 03/12/2017] [Accepted: 03/21/2017] [Indexed: 01/04/2023]
Abstract
Bre is a conserved cellular protein expressed in various tissues. Its major function includes DNA damage repair and anti-apoptosis. Recent studies indicate that Bre is potentially involved in stem cell differentiation although pathophysiological significance along with the molecular mechanisms is still unclear. Here, we report that Bre protein was substantially expressed in the bone tissue and its expression was highly upregulated during the osteogenic differentiation. To test a hypothesis that Bre plays functional roles in the process of osteogenic differentiation, we examined the expression of Bre in an osteoporosis mouse model. Compared with the normal bone tissue, Bre expression in osteoporotic bone was also significantly reduced. Moreover, knockdown of Bre in the mouse bone marrow mesenchymal cells significantly reduced the expression of osteogenic marker genes, the alkaline phosphatase activity, and the mineralization capacity, while overexpression of Bre greatly promoted the osteogenesis both in vitro and in vivo. Interestingly, we founded that knockdown of Bre led to activation of the p53 signaling pathways exhibited by increased p53, p21, and Mdm2. However, when we inhibited the p53 by siRNA silencing or pifithrin-α, the impaired osteogenesis caused by Bre knockdown was greatly restored. Finally, we found that Bre promoted the Mdm2-mediated p53 ubiquitination and degradation by physically interacting with p53. Taken together, our results revealed a novel function of Bre in osteoblast differentiation through modulating the stability of p53. Stem Cells 2017;35:1760-1772.
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Affiliation(s)
- Fujun Jin
- Guangzhou Jinan Biomedicine Research and Development Center, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, People's Republic of China
| | - Yiliang Wang
- Guangzhou Jinan Biomedicine Research and Development Center, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, People's Republic of China
| | - Xiaojing Wang
- Research Institute of Atherosclerotic Disease, Laboratory Animal Center, School of Medicine, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Yanting Wu
- Guangzhou Jinan Biomedicine Research and Development Center, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, People's Republic of China
| | - Xiaoyan Wang
- Guangzhou Jinan Biomedicine Research and Development Center, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, People's Republic of China
| | - Qiuying Liu
- Guangzhou Jinan Biomedicine Research and Development Center, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, People's Republic of China
| | - Yexuan Zhu
- Guangzhou Jinan Biomedicine Research and Development Center, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, People's Republic of China
| | - Enqi Liu
- Research Institute of Atherosclerotic Disease, Laboratory Animal Center, School of Medicine, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Jianglin Fan
- Department of Molecular Pathology, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Yamanashi, Japan
| | - Yifei Wang
- Guangzhou Jinan Biomedicine Research and Development Center, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, People's Republic of China
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24
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Huang JH, Ku WC, Chen YC, Chang YL, Chu CY. Dual mechanisms regulate the nucleocytoplasmic localization of human DDX6. Sci Rep 2017; 7:42853. [PMID: 28216671 PMCID: PMC5316971 DOI: 10.1038/srep42853] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 01/18/2017] [Indexed: 12/14/2022] Open
Abstract
DDX6 is a conserved DEAD-box protein (DBP) that plays central roles in cytoplasmic RNA regulation, including processing body (P-body) assembly, mRNA decapping, and translational repression. Beyond its cytoplasmic functions, DDX6 may also have nuclear functions because its orthologues are known to localize to nuclei in several biological contexts. However, it is unclear whether DDX6 is generally present in human cell nuclei, and the molecular mechanism underlying DDX6 subcellular distribution remains elusive. In this study, we showed that DDX6 is commonly present in the nuclei of human-derived cells. Our structural and molecular analyses deviate from the current model that the shuttling of DDX6 is directly mediated by the canonical nuclear localization signal (NLS) and nuclear export signal (NES), which are recognized and transported by Importin-α/β and CRM1, respectively. Instead, we show that DDX6 can be transported by 4E-T in a piggyback manner. Furthermore, we provide evidence for a novel nuclear targeting mechanism in which DDX6 enters the newly formed nuclei by "hitch-hiking" on mitotic chromosomes with its C-terminal domain during M phase progression. Together, our results indicate that the nucleocytoplasmic localization of DDX6 is regulated by these dual mechanisms.
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Affiliation(s)
- Jo-Hsi Huang
- Department of Life Science, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Wei-Chi Ku
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei 24205, Taiwan
| | - Yen-Chun Chen
- Department of Life Science, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Yi-Ling Chang
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei 24205, Taiwan
| | - Chia-Ying Chu
- Department of Life Science, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
- Center for Systems Biology, National Taiwan University, Taipei 10617, Taiwan
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25
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Lisberg A, Ellis R, Nicholson K, Moku P, Swarup A, Dhurjati P, Nohe A. Mathematical modeling of the effects of CK2.3 on mineralization in osteoporotic bone. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2017; 6:208-215. [PMID: 28181418 PMCID: PMC5351412 DOI: 10.1002/psp4.12154] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 11/02/2016] [Accepted: 11/03/2016] [Indexed: 12/17/2022]
Abstract
Osteoporosis is caused by decreased bone mineral density (BMD) and new treatments for this disease are desperately needed. Bone morphogenetic protein 2 (BMP2) is crucial for bone formation. The mimetic peptide CK2.3 acts downstream of BMP2 and increases BMD when injected systemically into the tail vein of mice. However, the most effective dosage needed to induce BMD in humans is unknown. We developed a mathematical model for CK2.3‐dependent bone mineralization. We used a physiologically based pharmacokinetic (PBPK) model to derive the CK2.3 concentration needed to increase BMD. Based on our results, the ideal dose of CK2.3 for a healthy individual to achieve the maximum increase of mineralization was about 409 µM injected in 500 µL volume, while dosage for osteoporosis patients was about 990 µM. This model showed that CK2.3 could increase the average area of bone mineralization in patients and in healthy adults.
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Affiliation(s)
- A Lisberg
- Department of Biomedical EngineeringUniversity of DelawareNewarkDelawareUSA
| | - R Ellis
- Department of Chemical and Biomolecular EngineeringUniversity of DelawareNewarkDelawareUSA
| | - K Nicholson
- Department of Mathematical SciencesUniversity of DelawareNewarkDelewareUSA
| | - P Moku
- Department of Biological SciencesUniversity of DelawareNewarkDelawareUSA
| | - A Swarup
- Department of Biological SciencesUniversity of DelawareNewarkDelawareUSA
| | - P Dhurjati
- Department of Chemical and Biomolecular EngineeringUniversity of DelawareNewarkDelawareUSA
- Department of Mathematical SciencesUniversity of DelawareNewarkDelewareUSA
- Department of Biological SciencesUniversity of DelawareNewarkDelawareUSA
| | - A Nohe
- Department of Biomedical EngineeringUniversity of DelawareNewarkDelawareUSA
- Department of Biological SciencesUniversity of DelawareNewarkDelawareUSA
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26
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Chen YF, Lin HC, Chuang KN, Lin CH, Yen HCS, Yeang CH. A quantitative model for the rate-limiting process of UGA alternative assignments to stop and selenocysteine codons. PLoS Comput Biol 2017; 13:e1005367. [PMID: 28178267 PMCID: PMC5323020 DOI: 10.1371/journal.pcbi.1005367] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 02/23/2017] [Accepted: 01/18/2017] [Indexed: 12/20/2022] Open
Abstract
Ambiguity in genetic codes exists in cases where certain stop codons are alternatively used to encode non-canonical amino acids. In selenoprotein transcripts, the UGA codon may either represent a translation termination signal or a selenocysteine (Sec) codon. Translating UGA to Sec requires selenium and specialized Sec incorporation machinery such as the interaction between the SECIS element and SBP2 protein, but how these factors quantitatively affect alternative assignments of UGA has not been fully investigated. We developed a model simulating the UGA decoding process. Our model is based on the following assumptions: (1) charged Sec-specific tRNAs (Sec-tRNASec) and release factors compete for a UGA site, (2) Sec-tRNASec abundance is limited by the concentrations of selenium and Sec-specific tRNA (tRNASec) precursors, and (3) all synthesis reactions follow first-order kinetics. We demonstrated that this model captured two prominent characteristics observed from experimental data. First, UGA to Sec decoding increases with elevated selenium availability, but saturates under high selenium supply. Second, the efficiency of Sec incorporation is reduced with increasing selenoprotein synthesis. We measured the expressions of four selenoprotein constructs and estimated their model parameters. Their inferred Sec incorporation efficiencies did not correlate well with their SECIS-SBP2 binding affinities, suggesting the existence of additional factors determining the hierarchy of selenoprotein synthesis under selenium deficiency. This model provides a framework to systematically study the interplay of factors affecting the dual definitions of a genetic codon. The “code book” of protein translation maps 43 = 64 triplets of RNA sequences (codons) into 20 canonical amino acids and the stop signal. This code book is universal in almost all organisms on earth. Selenoproteins consist of selenium-containing amino acids–selenocysteines (Sec)–that are not among the 20 canonical amino acids. The cells “borrow” a stop codon UGA to translate selenocysteines. Since UGA maps to two possible outcomes, the translation machinery can synthesize both full-length selenoproteins (when UGA encodes selenocysteine) and truncated peptide chains (when UGA encodes translational termination). Despite extensive study about selenoprotein synthesis mechanisms, a quantitative model for how cells allocate resources to synthesize each species is yet to appear. We propose a quantitative model that can explain the dependency of experimental observables such as protein stability and Sec incorporation efficiency by various factors such as selenium concentration and mRNA levels. Saturation of those quantities implies the existence of limiting factors such as mRNA transcripts and Sec-specific tRNAs. The match between model simulations and experimental data suggests that the cellular decision making of synthesizing the two species of proteins may follow simple first-order kinetics.
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Affiliation(s)
- Yen-Fu Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Hsiu-Chuan Lin
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | - Kai-Neng Chuang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | - Chih-Hsu Lin
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Hsueh-Chi S. Yen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
- * E-mail: (HCSY); (CHY)
| | - Chen-Hsiang Yeang
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
- * E-mail: (HCSY); (CHY)
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27
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Du W, Goldstein R, Jiang Y, Aly O, Cerchietti L, Melnick A, Elemento O. Effective Combination Therapies for B-cell Lymphoma Predicted by a Virtual Disease Model. Cancer Res 2017; 77:1818-1830. [PMID: 28130226 DOI: 10.1158/0008-5472.can-16-0476] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 12/10/2016] [Accepted: 01/23/2017] [Indexed: 12/15/2022]
Abstract
The complexity of cancer signaling networks limits the efficacy of most single-agent treatments and brings about challenges in identifying effective combinatorial therapies. In this study, we used chronic active B-cell receptor (BCR) signaling in diffuse large B-cell lymphoma as a model system to establish a computational framework to optimize combinatorial therapy in silico We constructed a detailed kinetic model of the BCR signaling network, which captured the known complex cross-talk between the NFκB, ERK, and AKT pathways and multiple feedback loops. Combining this signaling model with a data-derived tumor growth model, we predicted viability responses of many single drug and drug combinations in agreement with experimental data. Under this framework, we exhaustively predicted and ranked the efficacy and synergism of all possible combinatorial inhibitions of eleven currently targetable kinases in the BCR signaling network. Ultimately, our work establishes a detailed kinetic model of the core BCR signaling network and provides the means to explore the large space of possible drug combinations. Cancer Res; 77(8); 1818-30. ©2017 AACR.
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Affiliation(s)
- Wei Du
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - Rebecca Goldstein
- Hematology/Oncology Division, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Yanwen Jiang
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York.,Hematology/Oncology Division, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Omar Aly
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - Leandro Cerchietti
- Hematology/Oncology Division, Department of Medicine, Weill Cornell Medicine, New York, New York.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York
| | - Ari Melnick
- Hematology/Oncology Division, Department of Medicine, Weill Cornell Medicine, New York, New York.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York
| | - Olivier Elemento
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York. .,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York.,Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
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28
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Wu H, von Kamp A, Leoncikas V, Mori W, Sahin N, Gevorgyan A, Linley C, Grabowski M, Mannan AA, Stoy N, Stewart GR, Ward LT, Lewis DJM, Sroka J, Matsuno H, Klamt S, Westerhoff HV, McFadden J, Plant NJ, Kierzek AM. MUFINS: multi-formalism interaction network simulator. NPJ Syst Biol Appl 2016; 2:16032. [PMID: 28725480 PMCID: PMC5516860 DOI: 10.1038/npjsba.2016.32] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 07/27/2016] [Accepted: 08/29/2016] [Indexed: 12/19/2022] Open
Abstract
Systems Biology has established numerous approaches for mechanistic modeling of molecular networks in the cell and a legacy of models. The current frontier is the integration of models expressed in different formalisms to address the multi-scale biological system organization challenge. We present MUFINS (MUlti-Formalism Interaction Network Simulator) software, implementing a unique set of approaches for multi-formalism simulation of interaction networks. We extend the constraint-based modeling (CBM) framework by incorporation of linear inhibition constraints, enabling for the first time linear modeling of networks simultaneously describing gene regulation, signaling and whole-cell metabolism at steady state. We present a use case where a logical hypergraph model of a regulatory network is expressed by linear constraints and integrated with a Genome-Scale Metabolic Network (GSMN) of mouse macrophage. We experimentally validate predictions, demonstrating application of our software in an iterative cycle of hypothesis generation, validation and model refinement. MUFINS incorporates an extended version of our Quasi-Steady State Petri Net approach to integrate dynamic models with CBM, which we demonstrate through a dynamic model of cortisol signaling integrated with the human Recon2 GSMN and a model of nutrient dynamics in physiological compartments. Finally, we implement a number of methods for deriving metabolic states from ~omics data, including our new variant of the iMAT congruency approach. We compare our approach with iMAT through the analysis of 262 individual tumor transcriptomes, recovering features of metabolic reprogramming in cancer. The software provides graphics user interface with network visualization, which facilitates use by researchers who are not experienced in coding and mathematical modeling environments.
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Affiliation(s)
- Huihai Wu
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Axel von Kamp
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Vytautas Leoncikas
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Wataru Mori
- Graduate School of Science and Engineering and Faculty of Science, Yamaguchi University, Yoshida, Yamaguchi, Japan
| | - Nilgun Sahin
- Molecular Cell Physiology, VU University Amsterdam, Amsterdam, The Netherlands
| | | | - Catherine Linley
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Marek Grabowski
- Institute of Informatics, University of Warsaw, Warsaw, Poland
| | - Ahmad A Mannan
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Nicholas Stoy
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Graham R Stewart
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Lara T Ward
- Oncology DMPK, AstraZeneca, Alderley Park, Cheshire, UK
| | - David J M Lewis
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Jacek Sroka
- Institute of Informatics, University of Warsaw, Warsaw, Poland
| | - Hiroshi Matsuno
- Graduate School of Science and Engineering and Faculty of Science, Yamaguchi University, Yoshida, Yamaguchi, Japan
| | - Steffen Klamt
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Hans V Westerhoff
- Molecular Cell Physiology, VU University Amsterdam, Amsterdam, The Netherlands
- Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester, UK
- Synthetic Systems Biology, Netherlands Institute for Systems Biology, University of Amsterdam, Amsterdam, The Netherlands
| | - Johnjoe McFadden
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Nicholas J Plant
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Andrzej M Kierzek
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
- Simcyp Limited (a Certara Company), Sheffield, UK
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29
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Simulating the Manipulation of Various Biological Micro/Nanoparticles by Considering a Crowned Roller Geometry. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2016. [DOI: 10.1007/s13369-016-2150-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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30
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Blacker TS, Duchen MR. Investigating mitochondrial redox state using NADH and NADPH autofluorescence. Free Radic Biol Med 2016; 100:53-65. [PMID: 27519271 PMCID: PMC5145803 DOI: 10.1016/j.freeradbiomed.2016.08.010] [Citation(s) in RCA: 208] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 08/02/2016] [Accepted: 08/08/2016] [Indexed: 11/27/2022]
Abstract
The redox states of the NAD and NADP pyridine nucleotide pools play critical roles in defining the activity of energy producing pathways, in driving oxidative stress and in maintaining antioxidant defences. Broadly speaking, NAD is primarily engaged in regulating energy-producing catabolic processes, whilst NADP may be involved in both antioxidant defence and free radical generation. Defects in the balance of these pathways are associated with numerous diseases, from diabetes and neurodegenerative disease to heart disease and cancer. As such, a method to assess the abundance and redox state of these separate pools in living tissues would provide invaluable insight into the underlying pathophysiology. Experimentally, the intrinsic fluorescence of the reduced forms of both redox cofactors, NADH and NADPH, has been used for this purpose since the mid-twentieth century. In this review, we outline the modern implementation of these techniques for studying mitochondrial redox state in complex tissue preparations. As the fluorescence spectra of NADH and NADPH are indistinguishable, interpreting the signals resulting from their combined fluorescence, often labelled NAD(P)H, can be complex. We therefore discuss recent studies using fluorescence lifetime imaging microscopy (FLIM) which offer the potential to discriminate between the two separate pools. This technique provides increased metabolic information from cellular autofluorescence in biomedical investigations, offering biochemical insights into the changes in time-resolved NAD(P)H fluorescence signals observed in diseased tissues.
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Affiliation(s)
- Thomas S Blacker
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK; Department of Physics and Astronomy, University College London, London WC1E 6BT, UK
| | - Michael R Duchen
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
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Zeng C, Guo X, Long J, Kuchenbaecker KB, Droit A, Michailidou K, Ghoussaini M, Kar S, Freeman A, Hopper JL, Milne RL, Bolla MK, Wang Q, Dennis J, Agata S, Ahmed S, Aittomäki K, Andrulis IL, Anton-Culver H, Antonenkova NN, Arason A, Arndt V, Arun BK, Arver B, Bacot F, Barrowdale D, Baynes C, Beeghly-Fadiel A, Benitez J, Bermisheva M, Blomqvist C, Blot WJ, Bogdanova NV, Bojesen SE, Bonanni B, Borresen-Dale AL, Brand JS, Brauch H, Brennan P, Brenner H, Broeks A, Brüning T, Burwinkel B, Buys SS, Cai Q, Caldes T, Campbell I, Carpenter J, Chang-Claude J, Choi JY, Claes KBM, Clarke C, Cox A, Cross SS, Czene K, Daly MB, de la Hoya M, De Leeneer K, Devilee P, Diez O, Domchek SM, Doody M, Dorfling CM, Dörk T, Dos-Santos-Silva I, Dumont M, Dwek M, Dworniczak B, Egan K, Eilber U, Einbeigi Z, Ejlertsen B, Ellis S, Frost D, Lalloo F, Fasching PA, Figueroa J, Flyger H, Friedlander M, Friedman E, Gambino G, Gao YT, Garber J, García-Closas M, Gehrig A, Damiola F, Lesueur F, Mazoyer S, Stoppa-Lyonnet D, Giles GG, Godwin AK, Goldgar DE, González-Neira A, Greene MH, Guénel P, Haeberle L, Haiman CA, Hallberg E, Hamann U, Hansen TVO, Hart S, Hartikainen JM, Hartman M, Hassan N, Healey S, Hogervorst FBL, Verhoef S, Hendricks CB, Hillemanns P, Hollestelle A, Hulick PJ, Hunter DJ, Imyanitov EN, Isaacs C, Ito H, Jakubowska A, Janavicius R, Jaworska-Bieniek K, Jensen UB, John EM, Joly Beauparlant C, Jones M, Kabisch M, Kang D, Karlan BY, Kauppila S, Kerin MJ, Khan S, Khusnutdinova E, Knight JA, Konstantopoulou I, Kraft P, Kwong A, Laitman Y, Lambrechts D, Lazaro C, Le Marchand L, Lee CN, Lee MH, Lester J, Li J, Liljegren A, Lindblom A, Lophatananon A, Lubinski J, Mai PL, Mannermaa A, Manoukian S, Margolin S, Marme F, Matsuo K, McGuffog L, Meindl A, Menegaux F, Montagna M, Muir K, Mulligan AM, Nathanson KL, Neuhausen SL, Nevanlinna H, Newcomb PA, Nord S, Nussbaum RL, Offit K, Olah E, Olopade OI, Olswold C, Osorio A, Papi L, Park-Simon TW, Paulsson-Karlsson Y, Peeters S, Peissel B, Peterlongo P, Peto J, Pfeiler G, Phelan CM, Presneau N, Radice P, Rahman N, Ramus SJ, Rashid MU, Rennert G, Rhiem K, Rudolph A, Salani R, Sangrajrang S, Sawyer EJ, Schmidt MK, Schmutzler RK, Schoemaker MJ, Schürmann P, Seynaeve C, Shen CY, Shrubsole MJ, Shu XO, Sigurdson A, Singer CF, Slager S, Soucy P, Southey M, Steinemann D, Swerdlow A, Szabo CI, Tchatchou S, Teixeira MR, Teo SH, Terry MB, Tessier DC, Teulé A, Thomassen M, Tihomirova L, Tischkowitz M, Toland AE, Tung N, Turnbull C, van den Ouweland AMW, van Rensburg EJ, Ven den Berg D, Vijai J, Wang-Gohrke S, Weitzel JN, Whittemore AS, Winqvist R, Wong TY, Wu AH, Yannoukakos D, Yu JC, Pharoah PDP, Hall P, Chenevix-Trench G, Dunning AM, Simard J, Couch FJ, Antoniou AC, Easton DF, Zheng W. Identification of independent association signals and putative functional variants for breast cancer risk through fine-scale mapping of the 12p11 locus. Breast Cancer Res 2016; 18:64. [PMID: 27459855 PMCID: PMC4962376 DOI: 10.1186/s13058-016-0718-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 05/18/2016] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Multiple recent genome-wide association studies (GWAS) have identified a single nucleotide polymorphism (SNP), rs10771399, at 12p11 that is associated with breast cancer risk. METHOD We performed a fine-scale mapping study of a 700 kb region including 441 genotyped and more than 1300 imputed genetic variants in 48,155 cases and 43,612 controls of European descent, 6269 cases and 6624 controls of East Asian descent and 1116 cases and 932 controls of African descent in the Breast Cancer Association Consortium (BCAC; http://bcac.ccge.medschl.cam.ac.uk/ ), and in 15,252 BRCA1 mutation carriers in the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA). Stepwise regression analyses were performed to identify independent association signals. Data from the Encyclopedia of DNA Elements project (ENCODE) and the Cancer Genome Atlas (TCGA) were used for functional annotation. RESULTS Analysis of data from European descendants found evidence for four independent association signals at 12p11, represented by rs7297051 (odds ratio (OR) = 1.09, 95 % confidence interval (CI) = 1.06-1.12; P = 3 × 10(-9)), rs805510 (OR = 1.08, 95 % CI = 1.04-1.12, P = 2 × 10(-5)), and rs1871152 (OR = 1.04, 95 % CI = 1.02-1.06; P = 2 × 10(-4)) identified in the general populations, and rs113824616 (P = 7 × 10(-5)) identified in the meta-analysis of BCAC ER-negative cases and BRCA1 mutation carriers. SNPs rs7297051, rs805510 and rs113824616 were also associated with breast cancer risk at P < 0.05 in East Asians, but none of the associations were statistically significant in African descendants. Multiple candidate functional variants are located in putative enhancer sequences. Chromatin interaction data suggested that PTHLH was the likely target gene of these enhancers. Of the six variants with the strongest evidence of potential functionality, rs11049453 was statistically significantly associated with the expression of PTHLH and its nearby gene CCDC91 at P < 0.05. CONCLUSION This study identified four independent association signals at 12p11 and revealed potentially functional variants, providing additional insights into the underlying biological mechanism(s) for the association observed between variants at 12p11 and breast cancer risk.
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Grants
- U10 CA180868 NCI NIH HHS
- R01 CA140323 NCI NIH HHS
- R37 CA070867 NCI NIH HHS
- U10 CA027469 NCI NIH HHS
- U01 CA116167 NCI NIH HHS
- 16561 Cancer Research UK
- R03 CA173531 NCI NIH HHS
- G0700491 Medical Research Council
- N02CP11019 NCI NIH HHS
- 10124 Cancer Research UK
- UG1 CA189867 NCI NIH HHS
- N01 CN025403 NCI NIH HHS
- R01 CA176785 NCI NIH HHS
- RC4 CA153828 NCI NIH HHS
- U10 CA101165 NCI NIH HHS
- R01 CA142996 NCI NIH HHS
- P50 CA125183 NCI NIH HHS
- P01 CA087969 NCI NIH HHS
- UM1 CA164920 NCI NIH HHS
- P30 CA168524 NCI NIH HHS
- U01 CA161032 NCI NIH HHS
- R01 CA092447 NCI NIH HHS
- R01 CA058860 NCI NIH HHS
- 20861 Cancer Research UK
- K07 CA092044 NCI NIH HHS
- UL1 TR000124 NCATS NIH HHS
- 11174 Cancer Research UK
- R01 CA100374 NCI NIH HHS
- P30 CA008748 NCI NIH HHS
- R01 CA128978 NCI NIH HHS
- R01 CA064277 NCI NIH HHS
- R01 CA083855 NCI NIH HHS
- R01 CA047147 NCI NIH HHS
- P30 CA014089 NCI NIH HHS
- U19 CA148537 NCI NIH HHS
- P30 CA051008 NCI NIH HHS
- R01 CA116167 NCI NIH HHS
- R01 CA148667 NCI NIH HHS
- P50 CA116201 NCI NIH HHS
- 16565 Cancer Research UK
- 15106 Cancer Research UK
- U01 CA113916 NCI NIH HHS
- R01 CA063464 NCI NIH HHS
- U10 CA037517 NCI NIH HHS
- N02CP65504 NCI NIH HHS
- U01 CA063464 NCI NIH HHS
- R01 CA077398 NCI NIH HHS
- R01 CA054281 NCI NIH HHS
- R01 CA132839 NCI NIH HHS
- P30 CA068485 NCI NIH HHS
- R01 CA102776 NCI NIH HHS
- U01 CA058860 NCI NIH HHS
- 10118 Cancer Research UK
- U19 CA148112 NCI NIH HHS
- R01 CA149429 NCI NIH HHS
- U01 CA098758 NCI NIH HHS
- U19 CA148065 NCI NIH HHS
- R01 CA069664 NCI NIH HHS
- 001 World Health Organization
- UM1 CA182910 NCI NIH HHS
- U10 CA180822 NCI NIH HHS
- P30 CA006927 NCI NIH HHS
- R37 CA054281 NCI NIH HHS
- R01 CA047305 NCI NIH HHS
- 10119 Cancer Research UK
- National Institutes of Health
- Seventh Framework Programme
- National Cancer Institute
- U.S. Department of Defense
- Canadian Institutes of Health Research
- Susan G. Komen for the Cure
- Breast Cancer Research Foundation
- Ovarian Cancer Research Fund
- National Health and Medical Research Council
- New South Wales Cancer Council
- Victorian Health Promotion Foundation
- Victorian Breast Cancer Research Consortium
- Dutch Cancer Society
- Cancer Institute NSW
- National Breast Cancer Foundation
- Breast Cancer Research Trust
- Breakthrough Breast Cancer
- NIHR Comprehensive Biomedical Research Centre
- Guy's and St Thomas' NHS Foundation Trust
- Oxford Biomedical Research Centre
- Dietmar-Hopp Foundation
- Helmholtz Society
- Fondation de France
- Institut National Du Cancer
- Ligue Contre le Cancer
- Agence Nationale de la Recherche
- Danish Medical Research Council
- Instituto de Salud Carlos III
- Red Temática de Investigacióm Cooperativa en Cáncer
- Asociación Española Contra el Cáncer
- Fondo de Investigación Sanitario
- California Breast Cancer Research Fund
- Lon V Smith Foundation
- Baden-Württemberg Ministry of Science, Research and Arts
- Deutsche Krebshilfe
- Federal Ministry of Education and Research
- Deutsches Krebsforschungszentrum
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance
- Academy of Finland
- Finnish Cancer Society
- Ministry of Education, Culture, Sports, Science, and Technology
- Ministry of Health, Labour and Welfare
- Takeda Health Foundation
- German Federal Ministry of Research and Education
- Swedish Cancer Society
- Gustav V Jubilee Foundation
- Berth von Kantzows Stiftelse
- Cancer Fund of North Savo
- Finnish Cancer Organizations
- Queensland Cancer Fund
- Prostate Cancer Foundation of Australia (AU)
- Cancer Council of New South Wales
- Cancer Council of Victoria
- Cancer Council of Tasmania
- Cancer Council of South Australia
- U.S. Army Medical Research and Materiel Command
- National Health and Medical Research Council (AU)
- California Breast Cancer Research Program
- Stichting Tegen Kanker
- Hamburg Cancer Society
- Italian Associatin for Cancer Research
- David F and Margaret T Grohne Family Foundation
- Ting Tsung and Wei Fong Chao Foundation
- Robert and Kate Niehaus Clinical Cancer Genetics Initiative
- Quebec Breast Cancer Foundation
- Ministry of Economic Development, Innovation and Export Trade
- Malaysian Ministry of Science, Technology and Innovation
- Malaysian Ministry of Higher Education
- Cancer Resarch Initiatives Foundation
- Biomedical Research Council
- National Medical Research Council
- K G Jebsen Centre for Breast Cancer Research
- Research Council of Norway
- Researhc Council of Norway
- South Eastern Norway Health Authority
- Norwegian Cancer Socieety
- Finnish Cancer Foundation
- Sigrid Juselius Foundation
- Biobanking and Biomolecular Resources Research Infrastructure
- Marit and Hans Rausings Initiative Against Breast Cancer
- Yorkshire Cancer Research
- Sheffield Experimental Cancer Medicine Centre
- Ministry of Education, Science and Technology
- National Cancer Institute Thailand
- Stefanie Spielman Breast Cancer Fund
- Hellenic Cooperative Oncology Group
- Research Council of Lithuania
- Cancer Association of South Africa
- NEYE Foundation
- Spanish Association Against Cancer
- German Cancer Aid
- Ligue Nationale Contre le Cancer
- Jess and Mildred Fisher Center for Familial Cancer Research
- Swing Fore the Cure
- Netherlands Organization of Scientific Research
- Pink Ribbons Project
- Hungarian Research Grants
- Norwegian EEA Financial Mechanism
- Instituto de Salud Carlos III (ES)
- Canadian Breast Cancer Research Alliance
- Ministry for Health, Welfare and Family Affairs
- Andrew Sabin Research Fund
- Russian Federation for Basic Research
- Istituto Toscano Tumori
- Ministry of Higher Education
- Dr. Ralph and Marian Falk Medical Research Trust
- Entertainment Industry Fund National Women's Cancer Research Alliance
- Frieda G and Saul F Shapira BRCA-Associated Cancer Research Program
- American Cancer Society
- National Center for Advancing Translational Sciences
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Affiliation(s)
- Chenjie Zeng
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, 2525 West End Avenue, 8th Floor, Nashville, TN, 37203-1738, USA
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, 2525 West End Avenue, 8th Floor, Nashville, TN, 37203-1738, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, 2525 West End Avenue, 8th Floor, Nashville, TN, 37203-1738, USA
| | - Karoline B Kuchenbaecker
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Arnaud Droit
- Proteomics Center, CHU de Québec Research Center and Department of Molecular Medicine, Laval University, Quebec, Canada
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Maya Ghoussaini
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Siddhartha Kar
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Adam Freeman
- Department of Surgery, St Vincent's Hospital, Melbourne, VIC, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global health, The University of Melbourne, Melbourne, Australia
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global health, The University of Melbourne, Melbourne, Australia
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Simona Agata
- Immunology and Molecular Oncology Unit, Istituto Oncologico Veneto IOV - IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico), Padua, Italy
| | - Shahana Ahmed
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Kristiina Aittomäki
- Department of Clinical Genetics, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Hoda Anton-Culver
- Department of Epidemiology, University of California Irvine, Irvine, CA, USA
| | - Natalia N Antonenkova
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
| | - Adalgeir Arason
- Department of Pathology, Landspitali University Hospital and BMC (Biomedical Centre), Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Banu K Arun
- University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Brita Arver
- Department of Oncology, Karolinska University Hospital, Stockholm, Sweden
| | - Francois Bacot
- McGill University and Génome Québec Innovation Centre, Montréal, Canada
| | - Daniel Barrowdale
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Caroline Baynes
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Alicia Beeghly-Fadiel
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, 2525 West End Avenue, 8th Floor, Nashville, TN, 37203-1738, USA
| | - Javier Benitez
- Human Cancer Genetics Program, Spanish National Cancer Research Centre, Madrid, Spain
- Centro de Investigación en Red de Enfermedades Raras, Valencia, Spain
| | - Marina Bermisheva
- Institute of Biochemistry and Genetics, Ufa Scientific Center of Russian Academy of Sciences, Ufa, Russia
| | - Carl Blomqvist
- Department of Oncology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - William J Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, 2525 West End Avenue, 8th Floor, Nashville, TN, 37203-1738, USA
- International Epidemiology Institute, Rockville, MD, USA
| | - Natalia V Bogdanova
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia, Milan, Italy
| | - Anne-Lise Borresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- K.G. Jebsen Center for Breast Cancer Research, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Judith S Brand
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul Brennan
- International Agency for Research on Cancer, Lyon, France
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Annegien Broeks
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Thomas Brüning
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr University Bochum, Bochum, Germany
| | - Barbara Burwinkel
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
- Molecular Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Saundra S Buys
- Department of Medicine, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, 2525 West End Avenue, 8th Floor, Nashville, TN, 37203-1738, USA
| | - Trinidad Caldes
- Molecular Oncology Laboratory, Hospital Clinico San Carlos, IdISSC (El Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Ian Campbell
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Jane Carpenter
- Australian Breast Cancer Tissue Bank, Westmead Millennium Institute, University of Sydney, Sydney, Australia
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ji-Yeob Choi
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, South Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- Cancer Research Institute, Seoul National University, Seoul, South Korea
| | | | - Christine Clarke
- Westmead Millenium Institute for Medical Research, University of Sydney, Sydney, Australia
| | - Angela Cox
- Sheffield Cancer Research, Department of Oncology, University of Sheffield, Sheffield, UK
| | - Simon S Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mary B Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, Hospital Clinico San Carlos, IdISSC (El Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Kim De Leeneer
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Peter Devilee
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Orland Diez
- Oncogenetics Group, University Hospital Vall d'Hebron, Vall d'Hebron Institute of Oncology (VHIO) and Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Susan M Domchek
- Department of Medicine, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michele Doody
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | | | - Thilo Dörk
- Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Isabel Dos-Santos-Silva
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Martine Dumont
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center, Laval University, Québec City, Canada
| | - Miriam Dwek
- Department of Biomedical Sciences, Faculty of Science and Technology, University of Westminster, London, UK
| | | | - Kathleen Egan
- Division of Population Sciences, Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Ursula Eilber
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zakaria Einbeigi
- Department of Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Bent Ejlertsen
- Department of Oncology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Steve Ellis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Debra Frost
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Fiona Lalloo
- Genetic Medicine, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Peter A Fasching
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
- David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Jonine Figueroa
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Henrik Flyger
- Department of Breast Surgery, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Michael Friedlander
- ANZ GOTG Coordinating Centre, Australia New Zealand GOG, Camperdown, NSW, Australia
| | - Eitan Friedman
- Susanne Levy Gertner Oncogenetics Unit, Sheba Medical Center, Tel-Hashomer, Israel
| | - Gaetana Gambino
- Section of Genetic Oncology, Deparment of Laboratory Medicine, University and University Hospital of Pisa, Pisa, Italy
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China
| | - Judy Garber
- Cancer Risk and Prevention Clinic, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Andrea Gehrig
- Institute of Human Genetics, University Würzburg, Wurzburg, Germany
| | - Francesca Damiola
- INSERM U1052, CNRS UMR5286, Université Lyon, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Fabienne Lesueur
- Genetic Epidemiology of Cancer team, Inserm, U900, Institut Curie, Mines ParisTech, 75248, Paris, France
| | - Sylvie Mazoyer
- INSERM U1052, CNRS UMR5286, Université Lyon, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Dominique Stoppa-Lyonnet
- Department of Tumour Biology, Institut Curie, Paris, France
- Institut Curie, INSERM U830, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global health, The University of Melbourne, Melbourne, Australia
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - David E Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Anna González-Neira
- Human Cancer Genetics Program, Spanish National Cancer Research Centre, Madrid, Spain
| | - Mark H Greene
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Pascal Guénel
- Environmental Epidemiology of Cancer, Center for Research in Epidemiology and Population Health, INSERM, Villejuif, France
- University Paris-Sud, Villejuif, France
| | - Lothar Haeberle
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Emily Hallberg
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas V O Hansen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Steven Hart
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Jaana M Hartikainen
- Cancer Center, Kuopio University Hospital, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Mikael Hartman
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Department of Surgery, National University Health System, Singapore, Singapore
| | - Norhashimah Hassan
- Cancer Research Initiatives Foundation, Subang Jaya, Selangor, Malaysia
- Breast Cancer Research Unit, Cancer Research Institute, University Malaya Medical Centre, Kuala Lumpur, Malaysia
| | - Sue Healey
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | - Senno Verhoef
- Family Cancer Clinic, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Carolyn B Hendricks
- Suburban Hospital, Bethesda, MD, USA
- Care of City of Hope Clinical Cancer Genetics Community Research Network, Duarte, CA, USA
| | - Peter Hillemanns
- Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Antoinette Hollestelle
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Peter J Hulick
- Center for Medical Genetics, NorthShore University HealthSystem, Evanston, IL, USA
| | - David J Hunter
- Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | | | - Claudine Isaacs
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Hidemi Ito
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Aichi, Japan
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Ramunas Janavicius
- State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
| | | | - Uffe Birk Jensen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, N, Denmark
| | - Esther M John
- Department of Epidemiology, Cancer Prevention Institute of California, Fremont, CA, USA
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Charles Joly Beauparlant
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center and Laval University, Quebec City, QC, Canada
| | - Michael Jones
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Maria Kabisch
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daehee Kang
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, South Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- Cancer Research Institute, Seoul National University, Seoul, South Korea
| | - Beth Y Karlan
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Saila Kauppila
- Department of Pathology, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Michael J Kerin
- School of Medicine, National University of Ireland, Galway, Ireland
| | - Sofia Khan
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of Russian Academy of Sciences, Ufa, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Julia A Knight
- Prosserman Centre for Health Research, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Canada
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Irene Konstantopoulou
- Molecular Diagnostics Laboratory, IRRP, National Centre for Scientific Research "Demokritos", Athens, Greece
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - Ava Kwong
- The Hong Kong Hereditary Breast Cancer Family Registry, Cancer Genetics Center, Hong Kong Sanatorium and Hospital, Hong Kong, China
- Department of Surgery, The University of Hong Kong, Hong Kong, China
| | - Yael Laitman
- Susanne Levy Gertner Oncogenetics Unit, Sheba Medical Center, Tel-Hashomer, Israel
| | - Diether Lambrechts
- Vesalius Research Center, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Leuven, Belgium
| | - Conxi Lazaro
- Molecular Diagnostic Unit, Hereditary Cancer Program, IDIBELL (Bellvitge Biomedical Research Institute), Catalan Institute of Oncology, Barcelona, Spain
| | | | - Chuen Neng Lee
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Min Hyuk Lee
- Department of Surgery, Soonchunhyang University and Hospital, Seoul, South Korea
| | - Jenny Lester
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jingmei Li
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Annelie Liljegren
- Department of Oncology, Karolinska University Hospital, Stockholm, Sweden
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Artitaya Lophatananon
- Division of Health Sciences, Warwick Medical School, Warwick University, Coventry, UK
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Phuong L Mai
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Arto Mannermaa
- Cancer Center, Kuopio University Hospital, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale Tumori (INT), Milan, Italy
| | - Sara Margolin
- Department of Oncology - Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Frederik Marme
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases, University of Heidelberg, Heidelberg, Germany
| | - Keitaro Matsuo
- Department of Preventive Medicine, Kyushu University Faculty of Medical Sciences, Fukuoka, Japan
| | - Lesley McGuffog
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Alfons Meindl
- Division of Gynaecology and Obstetrics, Technische Universität München, Munich, Germany
| | - Florence Menegaux
- Environmental Epidemiology of Cancer, Center for Research in Epidemiology and Population Health, INSERM, Villejuif, France
- University Paris-Sud, Villejuif, France
| | - Marco Montagna
- Immunology and Molecular Oncology Unit, Istituto Oncologico Veneto IOV - IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico), Padua, Italy
| | - Kenneth Muir
- Division of Health Sciences, Warwick Medical School, Warwick University, Coventry, UK
- Institute of Population Health, University of Manchester, Manchester, UK
| | - Anna Marie Mulligan
- Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Katherine L Nathanson
- Department of Medicine, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Polly A Newcomb
- Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Silje Nord
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Robert L Nussbaum
- Department of Medicine and Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Kenneth Offit
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Edith Olah
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | - Olufunmilayo I Olopade
- Center for Clinical Cancer Genetics and Global Health, University of Chicago Medical Center, Chicago, IL, USA
| | - Curtis Olswold
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Ana Osorio
- Human Genetics Group, Human Cancer Genetics Program, Spanish National Cancer Centre (CNIO), Madrid, Spain
- Biomedical Network on Rare Diseases (CIBERER), Madrid, Spain
| | - Laura Papi
- Unit of Medical Genetics, Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Florence, Italy
| | | | | | | | - Bernard Peissel
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale Tumori (INT), Milan, Italy
| | - Paolo Peterlongo
- IFOM, Fondazione Istituto FIRC (Italian Foundation of Cancer Research) di Oncologia Molecolare, Milan, Italy
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Georg Pfeiler
- Department of Obstetrics and Gynecology, and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Catherine M Phelan
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Nadege Presneau
- Department of Biomedical Sciences, Faculty of Science and Technology, University of Westminster, London, UK
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale Tumori (INT), Milan, Italy
| | - Nazneen Rahman
- Section of Cancer Genetics, The Institute of Cancer Research, London, UK
| | - Susan J Ramus
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Muhammad Usman Rashid
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Basic Sciences, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH & RC), Lahore, Pakistan
| | - Gad Rennert
- Clalit National Israeli Cancer Control Center and Department of Community Medicine and Epidemiology, Carmel Medical Center and B. Rappaport Faculty of Medicine, Haifa, Israel
| | - Kerstin Rhiem
- Centre of Familial Breast and Ovarian Cancer, Department of Gynaecology and Obstetrics and Centre for Integrated Oncology (CIO), Center for Molecular Medicine Cologne (CMMC), University Hospital of Cologne, Cologne, Germany
| | - Anja Rudolph
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ritu Salani
- Obstetrics and Gynecology, Ohio State University College of Medicine, Columbus, OH, USA
| | | | - Elinor J Sawyer
- Research Oncology, Guy's Hospital, King's College London, London, UK
| | - Marjanka K Schmidt
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Rita K Schmutzler
- Division of Molecular Gyneco-Oncology, Department of Gynaecology and Obstetrics, University Hospital of Cologne, Cologne, Germany
- Center of Familial Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany
- Center for Integrated Oncology, University Hospital of Cologne, Cologne, Germany
- Center for Molecular Medicine, University Hospital of Cologne, Cologne, Germany
| | - Minouk J Schoemaker
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Peter Schürmann
- Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Caroline Seynaeve
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Chen-Yang Shen
- School of Public Health, China Medical University, Taichung, Taiwan
- Taiwan Biobank, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Martha J Shrubsole
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, 2525 West End Avenue, 8th Floor, Nashville, TN, 37203-1738, USA
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, 2525 West End Avenue, 8th Floor, Nashville, TN, 37203-1738, USA
| | - Alice Sigurdson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Christian F Singer
- Department of Obstetrics and Gynecology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Susan Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Penny Soucy
- Centre Hospitalier Universitaire de Québec Research Center and Laval University, Quebec City, QC, Canada
| | - Melissa Southey
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Parkville, VIC, Australia
| | | | - Anthony Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Csilla I Szabo
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sandrine Tchatchou
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, Canada
| | - Manuel R Teixeira
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
- Biomedical Sciences Institute (ICBAS), Porto University, Porto, Portugal
| | - Soo H Teo
- Cancer Research Initiatives Foundation, Subang Jaya, Selangor, Malaysia
- Breast Cancer Research Unit, Cancer Research Institute, University Malaya Medical Centre, Kuala Lumpur, Malaysia
| | - Mary Beth Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Daniel C Tessier
- McGill University and Génome Québec Innovation Centre, Montréal, Canada
| | - Alex Teulé
- Genetic Counseling Unit, Hereditary Cancer Program, IDIBELL (Bellvitge Biomedical Research Institute), Catalan Institute of Oncology, Barcelona, Spain
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, C, Denmark
| | | | - Marc Tischkowitz
- Program in Cancer Genetics, Departments of Human Genetics and Oncology, McGill University, Montreal, QC, Canada
- Currently at Medical School Cambridge University, Cambridge, UK
| | - Amanda E Toland
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Nadine Tung
- Department of Medical Oncology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Clare Turnbull
- Section of Cancer Genetics, The Institute of Cancer Research, London, UK
| | | | | | - David Ven den Berg
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Joseph Vijai
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Shan Wang-Gohrke
- Department of Obstetrics and Gynecology, University of Ulm, Ulm, Germany
| | - Jeffrey N Weitzel
- Clinical Cancer Genetics, for the City of Hope Clinical Cancer Genetics Community Research Network, Duarte, CA, USA
| | - Alice S Whittemore
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Department of Clinical Chemistry and Biocenter Oulu, University of Oulu, Oulu, Finland
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre NordLab, Oulu, Finland
| | - Tien Y Wong
- Singapore Eye Research Institute, National University of Singapore, Singapore, Singapore
| | - Anna H Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Drakoulis Yannoukakos
- Department of Medical Oncology, Papageorgiou Hospital, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| | - Jyh-Cherng Yu
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Georgia Chenevix-Trench
- Department of Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Peter MacCallum Cancer Center, The University of Melbourne, Melbourne, Australia
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center, Laval University, Québec City, Canada
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, 2525 West End Avenue, 8th Floor, Nashville, TN, 37203-1738, USA.
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Liu ZP. Identifying network-based biomarkers of complex diseases from high-throughput data. Biomark Med 2016; 10:633-50. [DOI: 10.2217/bmm-2015-0035] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In this work, we review the main available computational methods of identifying biomarkers of complex diseases from high-throughput data. The emerging omics techniques provide powerful alternatives to measure thousands of molecules in cells in parallel manners. The generated genomic, transcriptomic, proteomic, metabolomic and phenomic data provide comprehensive molecular and cellular information for detecting critical signals served as biomarkers by classifying disease phenotypic states. Networks are often employed to organize these profiles in the identification of biomarkers to deal with complex diseases in diagnosis, prognosis and therapy as well as mechanism deciphering from systematic perspectives. Here, we summarize some representative network-based bioinformatics methods in order to highlight the importance of computational strategies in biomarker discovery.
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Affiliation(s)
- Zhi-Ping Liu
- Department of Biomedical Engineering, School of Control Science & Engineering, Shandong University, Jinan, Shandong 250061, China
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Plant D, Webster A, Nair N, Oliver J, Smith SL, Eyre S, Hyrich KL, Wilson AG, Morgan AW, Isaacs JD, Worthington J, Barton A. Differential Methylation as a Biomarker of Response to Etanercept in Patients With Rheumatoid Arthritis. Arthritis Rheumatol 2016; 68:1353-60. [PMID: 26814849 PMCID: PMC4914881 DOI: 10.1002/art.39590] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 01/07/2016] [Indexed: 01/03/2023]
Abstract
Objective Biologic drug therapies represent a huge advance in the treatment of rheumatoid arthritis (RA). However, very good disease control is achieved in only 30% of patients, making identification of biomarkers of response a research priority. We undertook this study to test our hypothesis that differential DNA methylation patterns may provide biomarkers predictive of response to tumor necrosis factor inhibitor (TNFi) therapy in patients with RA. Methods An epigenome‐wide association study was performed on pretreatment whole blood DNA from patients with RA. Patients who displayed good response (n = 36) or no response (n = 36) to etanercept therapy at 3 months were selected. Differentially methylated positions were identified using linear regression. Variance of methylation at differentially methylated positions was assessed for correlation with cis‐acting single‐nucleotide polymorphisms (SNPs). A replication experiment for prioritized SNPs was performed in an independent cohort of 1,204 RA patients. Results Five positions that were differentially methylated between responder groups were identified, with a false discovery rate of <5%. The top 2 differentially methylated positions mapped to exon 7 of the LRPAP1 gene on chromosome 4 (cg04857395, P = 1.39 × 10−8 and cg26401028, P = 1.69 × 10−8). The A allele of the SNP rs3468 was correlated with higher levels of methylation for both of the top 2 differentially methylated positions (P = 2.63 × 10−7 and P = 1.05 × 10−6, respectively). Furthermore, the A allele of rs3468 was correlated with European League Against Rheumatism nonresponse in the discovery cohort (P = 0.03; n = 56) and in the independent replication cohort (P = 0.003; n = 1,204). Conclusion We identify DNA methylation as a potential biomarker of response to TNFi therapy, and we report the association between response and the LRPAP1 gene, which encodes a chaperone of low‐density lipoprotein receptor–related protein 1. Additional replication experiments in independent sample collections are now needed.
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Affiliation(s)
- Darren Plant
- NIHR Manchester Musculoskeletal Biomedical Research Unit, Manchester Academy of Health Sciences, and Central Manchester NHS Trust, Manchester, UK
| | - Amy Webster
- Arthritis Research UK Centre for Genetics and Genomics, University of Manchester, Manchester, UK
| | - Nisha Nair
- Arthritis Research UK Centre for Genetics and Genomics, University of Manchester, Manchester, UK
| | - James Oliver
- Arthritis Research UK Centre for Genetics and Genomics, University of Manchester, Manchester, UK
| | - Samantha L Smith
- Arthritis Research UK Centre for Genetics and Genomics, University of Manchester, Manchester, UK
| | - Steven Eyre
- Arthritis Research UK Centre for Genetics and Genomics, University of Manchester, Manchester, UK
| | - Kimme L Hyrich
- Arthritis Research UK Centre for Genetics and Genomics, University of Manchester, Manchester, UK
| | - Anthony G Wilson
- University College Dublin School of Medicine and Medical Science, and Conway Institute, Dublin, Ireland
| | - Ann W Morgan
- NIHR Leeds Musculoskeletal Biomedical Research Unit, Leeds Teaching Hospitals NHS Trust and Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | - John D Isaacs
- NIHR Newcastle Biomedical Research Centre in Ageing and Chronic Disease, Newcastle University, and Newcastle-Upon-Tyne NHS Foundation Trust, Newcastle-Upon-Tyne, UK
| | - Jane Worthington
- NIHR Manchester Musculoskeletal Biomedical Research Unit, Manchester Academy of Health Sciences, and Central Manchester NHS Trust, and Arthritis Research UK Centre for Genetics and Genomics, University of Manchester, Manchester, UK
| | - Anne Barton
- NIHR Manchester Musculoskeletal Biomedical Research Unit, Manchester Academy of Health Sciences, and Central Manchester NHS Trust, and Arthritis Research UK Centre for Genetics and Genomics, University of Manchester, Manchester, UK
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Rogers S, Fey D, McCloy RA, Parker BL, Mitchell NJ, Payne RJ, Daly RJ, James DE, Caldon CE, Watkins DN, Croucher DR, Burgess A. PP1 initiates the dephosphorylation of MASTL, triggering mitotic exit and bistability in human cells. J Cell Sci 2016; 129:1340-54. [PMID: 26872783 PMCID: PMC4852720 DOI: 10.1242/jcs.179754] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 02/08/2016] [Indexed: 12/23/2022] Open
Abstract
Entry into mitosis is driven by the phosphorylation of thousands of substrates, under the master control of Cdk1. During entry into mitosis, Cdk1, in collaboration with MASTL kinase, represses the activity of the major mitotic protein phosphatases, PP1 and PP2A, thereby ensuring mitotic substrates remain phosphorylated. For cells to complete and exit mitosis, these phosphorylation events must be removed, and hence, phosphatase activity must be reactivated. This reactivation of phosphatase activity presumably requires the inhibition of MASTL; however, it is not currently understood what deactivates MASTL and how this is achieved. In this study, we identified that PP1 is associated with, and capable of partially dephosphorylating and deactivating, MASTL during mitotic exit. Using mathematical modelling, we were able to confirm that deactivation of MASTL is essential for mitotic exit. Furthermore, small decreases in Cdk1 activity during metaphase are sufficient to initiate the reactivation of PP1, which in turn partially deactivates MASTL to release inhibition of PP2A and, hence, create a feedback loop. This feedback loop drives complete deactivation of MASTL, ensuring a strong switch-like activation of phosphatase activity during mitotic exit.
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Affiliation(s)
- Samuel Rogers
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Dirk Fey
- Systems Biology Ireland, University College Dublin, Dublin 4, Ireland
| | - Rachael A McCloy
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Benjamin L Parker
- The Charles Perkins Centre, School of Molecular Bioscience and Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Nicholas J Mitchell
- School of Chemistry, The University of Sydney, Sydney 2006, New South Wales, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney 2006, New South Wales, Australia
| | - Roger J Daly
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences Monash University, Clayton, Victoria 3800, Australia
| | - David E James
- The Charles Perkins Centre, School of Molecular Bioscience and Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - C Elizabeth Caldon
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia St. Vincent's Clinical School, Faculty of Medicine, UNSW, Darlinghurst 2010, New South Wales, Australia
| | - D Neil Watkins
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia St. Vincent's Clinical School, Faculty of Medicine, UNSW, Darlinghurst 2010, New South Wales, Australia Department of Thoracic Medicine, St Vincent's Hospital, Darlinghurst, New South Wales 2010, Australia
| | - David R Croucher
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia St. Vincent's Clinical School, Faculty of Medicine, UNSW, Darlinghurst 2010, New South Wales, Australia
| | - Andrew Burgess
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia St. Vincent's Clinical School, Faculty of Medicine, UNSW, Darlinghurst 2010, New South Wales, Australia
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Higdon R, Earl RK, Stanberry L, Hudac CM, Montague E, Stewart E, Janko I, Choiniere J, Broomall W, Kolker N, Bernier RA, Kolker E. The promise of multi-omics and clinical data integration to identify and target personalized healthcare approaches in autism spectrum disorders. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 19:197-208. [PMID: 25831060 DOI: 10.1089/omi.2015.0020] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Complex diseases are caused by a combination of genetic and environmental factors, creating a difficult challenge for diagnosis and defining subtypes. This review article describes how distinct disease subtypes can be identified through integration and analysis of clinical and multi-omics data. A broad shift toward molecular subtyping of disease using genetic and omics data has yielded successful results in cancer and other complex diseases. To determine molecular subtypes, patients are first classified by applying clustering methods to different types of omics data, then these results are integrated with clinical data to characterize distinct disease subtypes. An example of this molecular-data-first approach is in research on Autism Spectrum Disorder (ASD), a spectrum of social communication disorders marked by tremendous etiological and phenotypic heterogeneity. In the case of ASD, omics data such as exome sequences and gene and protein expression data are combined with clinical data such as psychometric testing and imaging to enable subtype identification. Novel ASD subtypes have been proposed, such as CHD8, using this molecular subtyping approach. Broader use of molecular subtyping in complex disease research is impeded by data heterogeneity, diversity of standards, and ineffective analysis tools. The future of molecular subtyping for ASD and other complex diseases calls for an integrated resource to identify disease mechanisms, classify new patients, and inform effective treatment options. This in turn will empower and accelerate precision medicine and personalized healthcare.
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Affiliation(s)
- Roger Higdon
- 1 Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute , Seattle, Washington
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Vaudel M, Verheggen K, Csordas A, Raeder H, Berven FS, Martens L, Vizcaíno JA, Barsnes H. Exploring the potential of public proteomics data. Proteomics 2016; 16:214-25. [PMID: 26449181 PMCID: PMC4738454 DOI: 10.1002/pmic.201500295] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 08/25/2015] [Accepted: 09/28/2015] [Indexed: 12/22/2022]
Abstract
In a global effort for scientific transparency, it has become feasible and good practice to share experimental data supporting novel findings. Consequently, the amount of publicly available MS-based proteomics data has grown substantially in recent years. With some notable exceptions, this extensive material has however largely been left untouched. The time has now come for the proteomics community to utilize this potential gold mine for new discoveries, and uncover its untapped potential. In this review, we provide a brief history of the sharing of proteomics data, showing ways in which publicly available proteomics data are already being (re-)used, and outline potential future opportunities based on four different usage types: use, reuse, reprocess, and repurpose. We thus aim to assist the proteomics community in stepping up to the challenge, and to make the most of the rapidly increasing amount of public proteomics data.
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Affiliation(s)
- Marc Vaudel
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Kenneth Verheggen
- Medical Biotechnology Center, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Attila Csordas
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Helge Raeder
- Department of Clinical Science, KG Jebsen Center for Diabetes Research, University of Bergen, Bergen, Norway
| | - Frode S Berven
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway
- Department of Clinical Medicine, KG Jebsen Centre for Multiple Sclerosis Research, University of Bergen, Bergen, Norway
| | - Lennart Martens
- Medical Biotechnology Center, VIB, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Juan A Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Harald Barsnes
- Proteomics Unit, Department of Biomedicine, University of Bergen, Bergen, Norway
- Department of Clinical Science, KG Jebsen Center for Diabetes Research, University of Bergen, Bergen, Norway
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Lv Z, Fan J, Zhang X, Huang Q, Han J, Wu F, Hu G, Guo M, Jin Y. Integrative genomic analysis of interleukin-36RN and its prognostic value in cancer. Mol Med Rep 2015; 13:1404-12. [PMID: 26676204 DOI: 10.3892/mmr.2015.4667] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Accepted: 10/28/2015] [Indexed: 11/05/2022] Open
Abstract
Interleukin (IL)-36RN, previously known as IL1-F5 and IL-1δ, shares a 360-kb region of chromosome 2q13 with members of IL-1 systems. IL-36RN encodes an anti-inflammatory cytokine, IL-36 receptor antagonist (IL-36Ra). In spite of IL-36Ra showing the highest homology to IL-1 receptor (IL-1R) antagonist, it differs from the latter in aspects including its binding to IL-lRrp2 but not to IL-1R1. IL-36RN is mainly expressed in epithelial cells and has important roles in inflammatory diseases. In the present study, IL-36RN was identified in the genomes of 27 species, including human, chimpanzee, mouse, horse and dolphin. Human IL-36RN was mainly expressed in the eye, head and neck, fetal heart, lung, testis, cervix and placenta; furthermore, it was highly expressed in bladder and parathyroid tumors. Furthermore, a total of 30 single nucleotide polymorphisms causing missense mutations were determined, which are considered to be the causes of various diseases, such as generalized pustular psoriasis. In addition, the link between IL-36RN and the prognosis of certain cancer types was revealed through meta-analysis. Tumor-associated transcriptional factors c-Fos, activator protein-1, c-Jun and nuclear factor κB were found to bind to the upstream region in the IL-36RN gene. This may indicate that IL-36RN is involved in tumorigenesis and tumor progression through the regulation of tumor-associated transcriptional factors. The present study identified IL-36RN in various species and investigated the associations between IL-36RN and cancer prognosis, which would determine whether IL-36RN drove the evolution of the various species with regard to tumorigenesis.
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Affiliation(s)
- Zhilei Lv
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of the Ministry of Health, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Jinshuo Fan
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of the Ministry of Health, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Xiuxiu Zhang
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of the Ministry of Health, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Qi Huang
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of the Ministry of Health, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Jieli Han
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of the Ministry of Health, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Feng Wu
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of the Ministry of Health, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Guorong Hu
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of the Ministry of Health, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Mengfei Guo
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of the Ministry of Health, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Yang Jin
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of the Ministry of Health, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
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Perez-Riverol Y, Alpi E, Wang R, Hermjakob H, Vizcaíno JA. Making proteomics data accessible and reusable: current state of proteomics databases and repositories. Proteomics 2015; 15:930-49. [PMID: 25158685 PMCID: PMC4409848 DOI: 10.1002/pmic.201400302] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 08/06/2014] [Accepted: 08/22/2014] [Indexed: 01/10/2023]
Abstract
Compared to other data-intensive disciplines such as genomics, public deposition and storage of MS-based proteomics, data are still less developed due to, among other reasons, the inherent complexity of the data and the variety of data types and experimental workflows. In order to address this need, several public repositories for MS proteomics experiments have been developed, each with different purposes in mind. The most established resources are the Global Proteome Machine Database (GPMDB), PeptideAtlas, and the PRIDE database. Additionally, there are other useful (in many cases recently developed) resources such as ProteomicsDB, Mass Spectrometry Interactive Virtual Environment (MassIVE), Chorus, MaxQB, PeptideAtlas SRM Experiment Library (PASSEL), Model Organism Protein Expression Database (MOPED), and the Human Proteinpedia. In addition, the ProteomeXchange consortium has been recently developed to enable better integration of public repositories and the coordinated sharing of proteomics information, maximizing its benefit to the scientific community. Here, we will review each of the major proteomics resources independently and some tools that enable the integration, mining and reuse of the data. We will also discuss some of the major challenges and current pitfalls in the integration and sharing of the data.
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Affiliation(s)
- Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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V A, Nayar PG, Murugesan R, Mary B, P D, Ahmed SSSJ. CardioGenBase: A Literature Based Multi-Omics Database for Major Cardiovascular Diseases. PLoS One 2015; 10:e0143188. [PMID: 26624015 PMCID: PMC4666633 DOI: 10.1371/journal.pone.0143188] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 11/01/2015] [Indexed: 12/27/2022] Open
Abstract
Cardiovascular diseases (CVDs) account for high morbidity and mortality worldwide. Both, genetic and epigenetic factors are involved in the enumeration of various cardiovascular diseases. In recent years, a vast amount of multi-omics data are accumulated in the field of cardiovascular research, yet the understanding of key mechanistic aspects of CVDs remain uncovered. Hence, a comprehensive online resource tool is required to comprehend previous research findings and to draw novel methodology for understanding disease pathophysiology. Here, we have developed a literature-based database, CardioGenBase, collecting gene-disease association from Pubmed and MEDLINE. The database covers major cardiovascular diseases such as cerebrovascular disease, coronary artery disease (CAD), hypertensive heart disease, inflammatory heart disease, ischemic heart disease and rheumatic heart disease. It contains ~1,500 cardiovascular disease genes from ~2,4000 research articles. For each gene, literature evidence, ontology, pathways, single nucleotide polymorphism, protein-protein interaction network, normal gene expression, protein expressions in various body fluids and tissues are provided. In addition, tools like gene-disease association finder and gene expression finder are made available for the users with figures, tables, maps and venn diagram to fit their needs. To our knowledge, CardioGenBase is the only database to provide gene-disease association for above mentioned major cardiovascular diseases in a single portal. CardioGenBase is a vital online resource to support genome-wide analysis, genetic, epigenetic and pharmacological studies.
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Affiliation(s)
- Alexandar V
- Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Kelambakkam 603 103, Tamil Nadu, India
| | - Pradeep G. Nayar
- Department of Cardiology, Chettinad Super Specialty Hospital, Chettinad Academy of Research and Education, Kelambakkam 603 103, Tamil Nadu, India
| | - R. Murugesan
- Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Kelambakkam 603 103, Tamil Nadu, India
| | - Beaulah Mary
- Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Kelambakkam 603 103, Tamil Nadu, India
| | - Darshana P
- Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Kelambakkam 603 103, Tamil Nadu, India
| | - Shiek S. S. J. Ahmed
- Department of Computational Biology, Drug discovery Lab, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Kelambakkam, 603 103, Tamil Nadu, India
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Kolker E, Janko I, Montague E, Higdon R, Stewart E, Choiniere J, Lai A, Eckert M, Broomall W, Kolker N. Finding Text-Supported Gene-to-Disease Co-appearances with MOPED-Digger. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 19:754-6. [DOI: 10.1089/omi.2015.0151] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Eugene Kolker
- High-Throughput Analysis Core, Seattle Children's Research Institute, Seattle, Washington
- CDO Analytics, , Seattle Children's Hospital, Seattle, Washington
- Data-Enabled Life Sciences Alliance (DELSA), Seattle, Washington
- Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute, Seattle, Washington
- Departments of Biomedical Informatics and Medical Education and Pediatrics, School of Medicine, University of Washington, Seattle, Washington
| | - Imre Janko
- High-Throughput Analysis Core, Seattle Children's Research Institute, Seattle, Washington
- CDO Analytics, , Seattle Children's Hospital, Seattle, Washington
- Data-Enabled Life Sciences Alliance (DELSA), Seattle, Washington
| | - Elizabeth Montague
- High-Throughput Analysis Core, Seattle Children's Research Institute, Seattle, Washington
- CDO Analytics, , Seattle Children's Hospital, Seattle, Washington
- Data-Enabled Life Sciences Alliance (DELSA), Seattle, Washington
- Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute, Seattle, Washington
| | - Roger Higdon
- High-Throughput Analysis Core, Seattle Children's Research Institute, Seattle, Washington
- CDO Analytics, , Seattle Children's Hospital, Seattle, Washington
- Data-Enabled Life Sciences Alliance (DELSA), Seattle, Washington
- Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute, Seattle, Washington
| | - Elizabeth Stewart
- CDO Analytics, , Seattle Children's Hospital, Seattle, Washington
- Data-Enabled Life Sciences Alliance (DELSA), Seattle, Washington
- Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute, Seattle, Washington
| | - John Choiniere
- High-Throughput Analysis Core, Seattle Children's Research Institute, Seattle, Washington
- Data-Enabled Life Sciences Alliance (DELSA), Seattle, Washington
- Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute, Seattle, Washington
| | - Aaron Lai
- High-Throughput Analysis Core, Seattle Children's Research Institute, Seattle, Washington
- CDO Analytics, , Seattle Children's Hospital, Seattle, Washington
- Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute, Seattle, Washington
- University of Pennsylvania, School of Arts and Sciences, Philadelphia, Pennsylvania
| | - Mary Eckert
- High-Throughput Analysis Core, Seattle Children's Research Institute, Seattle, Washington
- CDO Analytics, , Seattle Children's Hospital, Seattle, Washington
- Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute, Seattle, Washington
- Northeastern University, College of Science, Boston, Massachusetts
| | - William Broomall
- High-Throughput Analysis Core, Seattle Children's Research Institute, Seattle, Washington
- CDO Analytics, , Seattle Children's Hospital, Seattle, Washington
- Data-Enabled Life Sciences Alliance (DELSA), Seattle, Washington
| | - Natali Kolker
- High-Throughput Analysis Core, Seattle Children's Research Institute, Seattle, Washington
- CDO Analytics, , Seattle Children's Hospital, Seattle, Washington
- Data-Enabled Life Sciences Alliance (DELSA), Seattle, Washington
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Rizzetto S, Priami C, Csikász-Nagy A. Qualitative and Quantitative Protein Complex Prediction Through Proteome-Wide Simulations. PLoS Comput Biol 2015; 11:e1004424. [PMID: 26492574 PMCID: PMC4619657 DOI: 10.1371/journal.pcbi.1004424] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 06/22/2015] [Indexed: 12/18/2022] Open
Abstract
Despite recent progress in proteomics most protein complexes are still unknown. Identification of these complexes will help us understand cellular regulatory mechanisms and support development of new drugs. Therefore it is really important to establish detailed information about the composition and the abundance of protein complexes but existing algorithms can only give qualitative predictions. Herein, we propose a new approach based on stochastic simulations of protein complex formation that integrates multi-source data--such as protein abundances, domain-domain interactions and functional annotations--to predict alternative forms of protein complexes together with their abundances. This method, called SiComPre (Simulation based Complex Prediction), achieves better qualitative prediction of yeast and human protein complexes than existing methods and is the first to predict protein complex abundances. Furthermore, we show that SiComPre can be used to predict complexome changes upon drug treatment with the example of bortezomib. SiComPre is the first method to produce quantitative predictions on the abundance of molecular complexes while performing the best qualitative predictions. With new data on tissue specific protein complexes becoming available SiComPre will be able to predict qualitative and quantitative differences in the complexome in various tissue types and under various conditions.
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Affiliation(s)
- Simone Rizzetto
- The Microsoft Research-University of Trento Centre for Computational Systems Biology, Rovereto, Italy
| | - Corrado Priami
- The Microsoft Research-University of Trento Centre for Computational Systems Biology, Rovereto, Italy
- Department of Mathematics, University of Trento, Povo (TN), Italy
- * E-mail: (CP); (ACN)
| | - Attila Csikász-Nagy
- Department of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
- Randall Division of Cell and Molecular Biophysics and Institute for Mathematical and Molecular Biomedicine, King's College London, London, United Kingdom
- * E-mail: (CP); (ACN)
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Perera MTPR, Higdon R, Richards DA, Silva MA, Murphy N, Kolker E, Mirza DF. Biomarker differences between cadaveric grafts used in human orthotopic liver transplantation as identified by coulometric electrochemical array detection (CEAD) metabolomics. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 18:767-77. [PMID: 25353146 DOI: 10.1089/omi.2014.0094] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Metabolomics in systems biology research unravels intracellular metabolic changes by high throughput methods, but such studies focusing on liver transplantation (LT) are limited. Microdialysate samples of liver grafts from donors after circulatory death (DCD; n=13) and brain death (DBD; n=27) during cold storage and post-reperfusion phase were analyzed through coulometric electrochemical array detection (CEAD) for identification of key metabolomics changes. Metabolite peak differences between the graft types at cold phase, post-reperfusion trends, and in failed allografts, were identified against reference chromatograms. In the cold phase, xanthine, uric acid, and kynurenine were overexpressed in DCD by 3-fold, and 3-nitrotyrosine (3-NT) and 4-hydroxy-3-methoxymandelic acid (HMMA) in DBD by 2-fold (p<0.05). In both grafts, homovanillic acid and methionine increased by 20%-30% with each 100 min increase in cold ischemia time (p<0.05). Uric acid expression was significantly different in DCD post-reperfusion. Failed allografts had overexpression of reduced glutathione and kynurenine (cold phase) and xanthine (post-reperfusion) (p<0.05). This differential expression of metabolites between graft types is a novel finding, meanwhile identification of overexpression of kynurenine in DCD grafts and in failed allografts is unique. Further studies should examine kynurenine as a potential biomarker predicting graft function, its causation, and actions on subsequent clinical outcomes.
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Affiliation(s)
- M Thamara P R Perera
- 1 The Liver Unit, Queen Elizabeth Hospital Birmingham , Edgbaston, Birmingham, United Kingdom
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Toga AW, Dinov ID. Sharing big biomedical data. JOURNAL OF BIG DATA 2015; 2:7. [PMID: 26929900 PMCID: PMC4768816 DOI: 10.1186/s40537-015-0016-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 04/28/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND The promise of Big Biomedical Data may be offset by the enormous challenges in handling, analyzing, and sharing it. In this paper, we provide a framework for developing practical and reasonable data sharing policies that incorporate the sociological, financial, technical and scientific requirements of a sustainable Big Data dependent scientific community. FINDINGS Many biomedical and healthcare studies may be significantly impacted by using large, heterogeneous and incongruent datasets; however there are significant technical, social, regulatory, and institutional barriers that need to be overcome to ensure the power of Big Data overcomes these detrimental factors. CONCLUSIONS Pragmatic policies that demand extensive sharing of data, promotion of data fusion, provenance, interoperability and balance security and protection of personal information are critical for the long term impact of translational Big Data analytics.
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Affiliation(s)
- Arthur W Toga
- />Laboratory of Neuro Imaging, Institute of Neuroimaging and Informatics, Keck School of Medicine of USC, University of Sothern California, 2001 North Soto Street-Room 102, Los Angeles, CA 90033 USA
| | - Ivo D Dinov
- />Statistics Online Computaitonal Resource, University of Michigan, UMSN, 400 North Ingalls, Room 4341, Ann Arbor, 48109-5482 MI USA
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Profiling of urinary proteins in Karan Fries cows reveals more than 1550 proteins. J Proteomics 2015; 127:193-201. [PMID: 26021477 DOI: 10.1016/j.jprot.2015.05.026] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 05/18/2015] [Accepted: 05/21/2015] [Indexed: 12/15/2022]
Abstract
Urine is a non-invasive source of biological fluid, which reflects the physiological status of the mammals. We have profiled the cow urinary proteome and analyzed its functional significance. The urine collected from three healthy cows was concentrated by diafiltration (DF) followed by protein extraction using three methods, namely methanol, acetone, and ammonium sulphate (AS) precipitation and Proteo Spin urine concentration kit (PS). The quality of the protein was assessed by two-dimensional gel electrophoresis (2DE). In-gel digestion method revealed more proteins (1191) in comparison to in-solution digestion method (541). Collectively, 938, 606 and 444 proteins were identified in LC-MS/MS after in-gel and in-solution tryptic digestion of proteins prepared by AS, PS and DF methods, respectively resulting in identification of a total of 1564 proteins. Gene ontology (GO) using Panther7.0 grouped the majority of the proteins into cytoplasmic (location), catalytic activity (function), and metabolism (biological processes), while Cytoscape grouped proteins into complement and coagulation cascades; protease inhibitor activity and wound healing. Functional significance of few selected proteins seems to play important role in their physiology. Comparative analysis with human urine revealed 315 overlapping proteins. This study reports for the first time evidence of more than 1550 proteins in urine of healthy cow donors. This article is part of a Special Issue entitled: Proteomics in India.
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Huang YT, Liang L, Moffatt MF, Cookson WOCM, Lin X. iGWAS: Integrative Genome-Wide Association Studies of Genetic and Genomic Data for Disease Susceptibility Using Mediation Analysis. Genet Epidemiol 2015; 39:347-56. [PMID: 25997986 DOI: 10.1002/gepi.21905] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 03/23/2015] [Accepted: 04/07/2015] [Indexed: 12/20/2022]
Abstract
Genome-wide association studies (GWAS) have been a standard practice in identifying single nucleotide polymorphisms (SNPs) for disease susceptibility. We propose a new approach, termed integrative GWAS (iGWAS) that exploits the information of gene expressions to investigate the mechanisms of the association of SNPs with a disease phenotype, and to incorporate the family-based design for genetic association studies. Specifically, the relations among SNPs, gene expression, and disease are modeled within the mediation analysis framework, which allows us to disentangle the genetic effect on a disease phenotype into two parts: an effect mediated through a gene expression (mediation effect, ME) and an effect through other biological mechanisms or environment-mediated mechanisms (alternative effect, AE). We develop omnibus tests for the ME and AE that are robust to underlying true disease models. Numerical studies show that the iGWAS approach is able to facilitate discovering genetic association mechanisms, and outperforms the SNP-only method for testing genetic associations. We conduct a family-based iGWAS of childhood asthma that integrates genetic and genomic data. The iGWAS approach identifies six novel susceptibility genes (MANEA, MRPL53, LYCAT, ST8SIA4, NDFIP1, and PTCH1) using the omnibus test with false discovery rate less than 1%, whereas no gene using SNP-only analyses survives with the same cut-off. The iGWAS analyses further characterize that genetic effects of these genes are mostly mediated through their gene expressions. In summary, the iGWAS approach provides a new analytic framework to investigate the mechanism of genetic etiology, and identifies novel susceptibility genes of childhood asthma that were biologically meaningful.
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Affiliation(s)
- Yen-Tsung Huang
- Departments of Epidemiology and Biostatistics, Brown University, Providence, Rhode Island, United States of America
| | - Liming Liang
- Departments of Epidemiology and Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Miriam F Moffatt
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | | | - Xihong Lin
- Departments of Epidemiology and Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
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Higdon R, Kolker E. Can "normal" protein expression ranges be estimated with high-throughput proteomics? J Proteome Res 2015; 14:2398-407. [PMID: 25877823 DOI: 10.1021/acs.jproteome.5b00176] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Although biological science discovery often involves comparing conditions to a normal state, in proteomics little is actually known about normal. Two Human Proteome studies featured in Nature offer new insights into protein expression and an opportunity to assess how high-throughput proteomics measures normal protein ranges. We use data from these studies to estimate technical and biological variability in protein expression and compare them to other expression data sets from normal tissue. Results show that measured protein expression across same-tissue replicates vary by ±4- to 10-fold for most proteins. Coefficients of variation (CV) for protein expression measurements range from 62% to 117% across different tissue experiments; however, adjusting for technical variation reduced this variability by as much as 50%. In addition, the CV could also be reduced by limiting comparisons to proteins with at least 3 or more unique peptide identifications as the CV was on average 33% lower than for proteins with 2 or fewer peptide identifications. We also selected 13 housekeeping proteins and genes that were expressed across all tissues with low variability to determine their utility as a reference set for normalization and comparative purposes. These results present the first step toward estimating normal protein ranges by determining the variability in expression measurements through combining publicly available data. They support an approach that combines standard protocols with replicates of normal tissues to estimate normal protein ranges for large numbers of proteins and tissues. This would be a tremendous resource for normal cellular physiology and comparisons of proteomics studies.
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Affiliation(s)
- Roger Higdon
- †Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute, Seattle, Washington 98101, United States.,‡CDO Analytics, Seattle Children's Hospital, Seattle, Washington 98101, United States
| | - Eugene Kolker
- †Bioinformatics and High-Throughput Analysis Laboratory, Seattle Children's Research Institute, Seattle, Washington 98101, United States.,‡CDO Analytics, Seattle Children's Hospital, Seattle, Washington 98101, United States.,§Departments of Biomedical Informatics and Medical Education and Pediatrics, University of Washington, Seattle, Washington 98195, United States.,∥Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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Chen T, Zhao J, Ma J, Zhu Y. Web resources for mass spectrometry-based proteomics. GENOMICS PROTEOMICS & BIOINFORMATICS 2015; 13:36-9. [PMID: 25721607 PMCID: PMC4411487 DOI: 10.1016/j.gpb.2015.01.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 01/22/2015] [Accepted: 01/28/2015] [Indexed: 12/11/2022]
Abstract
With the development of high-resolution and high-throughput mass spectrometry (MS) technology, a large quantum of proteomic data is continually being generated. Collecting and sharing these data are a challenge that requires immense and sustained human effort. In this report, we provide a classification of important web resources for MS-based proteomics and present rating of these web resources, based on whether raw data are stored, whether data submission is supported, and whether data analysis pipelines are provided. These web resources are important for biologists involved in proteomics research.
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Affiliation(s)
- Tao Chen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Jie Zhao
- Biological Information College, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Jie Ma
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Yunping Zhu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China.
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Colangelo CM, Shifman M, Cheung KH, Stone KL, Carriero NJ, Gulcicek EE, Lam TT, Wu T, Bjornson RD, Bruce C, Nairn AC, Rinehart J, Miller PL, Williams KR. YPED: an integrated bioinformatics suite and database for mass spectrometry-based proteomics research. GENOMICS, PROTEOMICS & BIOINFORMATICS 2015; 13:25-35. [PMID: 25712262 PMCID: PMC4411476 DOI: 10.1016/j.gpb.2014.11.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 10/13/2014] [Accepted: 11/11/2014] [Indexed: 10/25/2022]
Abstract
We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database (YPED) that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a single laboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography-tandem mass spectrometry (LC-MS/MS) database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring (MRM)/selective reaction monitoring (SRM) assay development. We have linked YPED's database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results.
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Affiliation(s)
- Christopher M Colangelo
- W.M. Keck Foundation Biotechnology Resource Laboratory, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA.
| | - Mark Shifman
- Yale Center for Medical Informatics, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Anesthesiology, School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Kei-Hoi Cheung
- Yale Center for Medical Informatics, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Emergency Medicine, School of Medicine, Yale University, New Haven, CT 06510, USA; VA Connecticut Healthcare System, West Haven, CT 06516, USA
| | - Kathryn L Stone
- W.M. Keck Foundation Biotechnology Resource Laboratory, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Nicholas J Carriero
- W.M. Keck Foundation Biotechnology Resource Laboratory, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA; Yale Center for Genome Analysis, West Campus, Yale University, Orange, CT 06477, USA
| | - Erol E Gulcicek
- W.M. Keck Foundation Biotechnology Resource Laboratory, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA
| | - TuKiet T Lam
- W.M. Keck Foundation Biotechnology Resource Laboratory, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Terence Wu
- W.M. Keck Foundation Biotechnology Resource Laboratory, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA; Yale West Campus Analytical Core, West Campus, Yale University, West Haven, CT 06516, USA
| | - Robert D Bjornson
- W.M. Keck Foundation Biotechnology Resource Laboratory, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA; Yale Center for Genome Analysis, West Campus, Yale University, Orange, CT 06477, USA
| | - Can Bruce
- W.M. Keck Foundation Biotechnology Resource Laboratory, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA; Yale Bioinformatics Resource, School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Angus C Nairn
- Department of Psychiatry, School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Jesse Rinehart
- Department of Cellular & Molecular Physiology, School of Medicine, Yale University, New Haven, CT 06510, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Perry L Miller
- Yale Center for Medical Informatics, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Anesthesiology, School of Medicine, Yale University, New Haven, CT 06510, USA; VA Connecticut Healthcare System, West Haven, CT 06516, USA
| | - Kenneth R Williams
- W.M. Keck Foundation Biotechnology Resource Laboratory, School of Medicine, Yale University, New Haven, CT 06510, USA; Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA
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49
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Ramirez VP, Stamatis M, Shmukler A, Aneskievich BJ. Basal and stress-inducible expression of HSPA6 in human keratinocytes is regulated by negative and positive promoter regions. Cell Stress Chaperones 2015; 20:95-107. [PMID: 25073946 PMCID: PMC4255259 DOI: 10.1007/s12192-014-0529-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 07/17/2014] [Accepted: 07/18/2014] [Indexed: 01/08/2023] Open
Abstract
Epidermal keratinocytes serve as the primary barrier between the body and environmental stressors. They are subjected to numerous stress events and are likely to respond with a repertoire of heat shock proteins (HSPs). HSPA6 (HSP70B') is described in other cell types with characteristically low to undetectable basal expression, but is highly stress induced. Despite this response in other cells, little is known about its control in keratinocytes. We examined endogenous human keratinocyte HSPA6 expression and localized some responsible transcription factor sites in a cloned HSPA6 3 kb promoter. Using promoter 5' truncations and deletions, negative and positive regulatory regions were found throughout the 3 kb promoter. A region between -346 and -217 bp was found to be crucial to HSPA6 basal expression and stress inducibility. Site-specific mutations and DNA-binding studies show that a previously uncharacterized AP1 site contributes to the basal expression and maximal stress induction of HSPA6. Additionally, a new heat shock element (HSE) within this region was defined. While this element mediates increased transcriptional response in thermally stressed HaCaT keratinocytes, it preferentially binds a stress-inducible factor other than heat shock factor (HSF)1 or HSF2. Intriguingly, this newly characterized HSPA6 HSE competes HSF1 binding a consensus HSE and binds both HSF1 and HSF2 from other epithelial cells. Taken together, our results demonstrate that the HSPA6 promoter contains essential negative and positive promoter regions and newly identified transcription factor targets, which are key to the basal and stress-inducible expression of HSPA6. Furthermore, these results suggest that an HSF-like factor may preferentially bind this newly identified HSPA6 HSE in HaCaT cells.
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Affiliation(s)
- Vincent P. Ramirez
- />Graduate Program in Pharmacology and Toxicology, Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269-3092 USA
| | - Michael Stamatis
- />Doctor of Pharmacy Program, School of Pharmacy, University of Connecticut, Storrs, CT 06269-3092 USA
| | - Anastasia Shmukler
- />Doctor of Pharmacy Program, School of Pharmacy, University of Connecticut, Storrs, CT 06269-3092 USA
| | - Brian J. Aneskievich
- />Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, U-3092, 69 North Eagleville Road, Storrs, CT 06269-3092 USA
- />University of Connecticut Stem Cell Institute, Storrs, CT 06269-3092 USA
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50
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Morgan PG, Higdon R, Kolker N, Bauman AT, Ilkayeva O, Newgard CB, Kolker E, Steele LM, Sedensky MM. Comparison of proteomic and metabolomic profiles of mutants of the mitochondrial respiratory chain in Caenorhabditis elegans. Mitochondrion 2014; 20:95-102. [PMID: 25530493 DOI: 10.1016/j.mito.2014.12.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 09/10/2014] [Accepted: 12/10/2014] [Indexed: 01/06/2023]
Abstract
Single-gene mutations that disrupt mitochondrial respiratory chain function in Caenorhabditis elegans change patterns of protein expression and metabolites. Our goal was to develop useful molecular fingerprints employing adaptable techniques to recognize mitochondrial defects in the electron transport chain. We analyzed mutations affecting complex I, complex II, or ubiquinone synthesis and discovered overarching patterns in the response of C. elegans to mitochondrial dysfunction across all of the mutations studied. These patterns are in KEGG pathways conserved from C. elegans to mammals, verifying that the nematode can serve as a model for mammalian disease. In addition, specific differences exist between mutants that may be useful in diagnosing specific mitochondrial diseases in patients.
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Affiliation(s)
- P G Morgan
- Department of Anesthesiology and Pain Medicine, University of Washington, USA; Center for Developmental Therapeutics, Seattle Children's Research Institute, USA.
| | - R Higdon
- Bioinformatics and High-throughput Analysis Laboratory, USA; High-throughput Analysis Core, Seattle Children's Research Institute, USA; Data-Enabled Life Sciences Alliance (DELSA Global), USA
| | - N Kolker
- High-throughput Analysis Core, Seattle Children's Research Institute, USA; Data-Enabled Life Sciences Alliance (DELSA Global), USA
| | - A T Bauman
- Bioinformatics and High-throughput Analysis Laboratory, USA
| | - O Ilkayeva
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA; Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - C B Newgard
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA; Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - E Kolker
- Bioinformatics and High-throughput Analysis Laboratory, USA; High-throughput Analysis Core, Seattle Children's Research Institute, USA; Data-Enabled Life Sciences Alliance (DELSA Global), USA; Department of Biomedical Informatics & Medical Education, University of Washington, Seattle, WA, USA; Department of Pediatrics, University of Washington, Seattle, WA, USA; Department of Chemistry and Chemical Biology, College of Science, Northeastern University, Boston, MA 02115, USA
| | - L M Steele
- Center for Developmental Therapeutics, Seattle Children's Research Institute, USA
| | - M M Sedensky
- Department of Anesthesiology and Pain Medicine, University of Washington, USA; Center for Developmental Therapeutics, Seattle Children's Research Institute, USA
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