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In silico analysis decodes transthyretin (TTR) binding and thyroid disrupting effects of per- and polyfluoroalkyl substances (PFAS). Arch Toxicol 2023; 97:755-768. [PMID: 36566436 PMCID: PMC9968702 DOI: 10.1007/s00204-022-03434-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 12/13/2022] [Indexed: 12/26/2022]
Abstract
Transthyretin (TTR) is a homo-tetramer protein involved in the transport of thyroid hormone (thyroxine; T4) in the plasma and cerebrospinal fluid. Many pollutants have been shown to bind to TTR, which could be alarming as disruption in the thyroid hormone system can lead to several physiological problems. It is also indicated that the monomerization of tetramer and destabilization of monomer can lead to amyloidogenesis. Many compounds are identified that can bind to tetramer and stabilize the tetramer leading to the inhibition of amyloid fibril formation. Other compounds are known to bind tetramer and induce amyloid fibril formation. Among the pollutants, per- and polyfluoroalkyl substances (PFAS) are known to disrupt the thyroid hormone system. The molecular mechanisms of thyroid hormone disruption could be diverse, as some are known to bind with thyroid hormone receptors, and others can bind to membrane transporters. Binding to TTR could also be one of the important pathways to alter thyroid signaling. However, the molecular interactions that drive thyroid-disrupting effects of long-chain and short-chain PFASs are not comprehensively understood at the molecular level. In this study, using a computational approach, we show that carbon chain length and functional group in PFASs are structural determinants, in which longer carbon chains of PFASs and sulfur-containing PFASs favor stronger interactions with TTR than their shorter-chained counterparts. Interestingly, short-chain PFAS also showed strong binding capacity, and the interaction energy for some was as close to the longer-chain PFAS. This suggests that short-chain PFASs are not completely safe, and their use and build-up in the environment should be carefully regulated. Of note, TTR homologs analysis suggests that thyroid-disrupting effects of PFASs could be most likely translated to TTR-like proteins and other species.
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2
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Gundacker C, Audouze K, Widhalm R, Granitzer S, Forsthuber M, Jornod F, Wielsøe M, Long M, Halldórsson TI, Uhl M, Bonefeld-Jørgensen EC. Reduced Birth Weight and Exposure to Per- and Polyfluoroalkyl Substances: A Review of Possible Underlying Mechanisms Using the AOP-HelpFinder. TOXICS 2022; 10:toxics10110684. [PMID: 36422892 PMCID: PMC9699222 DOI: 10.3390/toxics10110684] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 05/14/2023]
Abstract
Prenatal exposure to per- and polyfluorinated substances (PFAS) may impair fetal growth. Our knowledge of the underlying mechanisms is incomplete. We used the Adverse Outcome Pathway (AOP)-helpFinder tool to search PubMed for studies published until March 2021 that examined PFAS exposure in relation to birth weight, oxidative stress, hormones/hormone receptors, or growth signaling pathways. Of these 1880 articles, 106 experimental studies remained after abstract screening. One clear finding is that PFAS are associated with oxidative stress in in vivo animal studies and in vitro studies. It appears that PFAS-induced reactive-oxygen species (ROS) generation triggers increased peroxisome proliferator-activated receptor (PPAR)γ expression and activation of growth signaling pathways, leading to hyperdifferentiation of pre-adipocytes. Fewer proliferating pre-adipocytes result in lower adipose tissue weight and in this way may reduce birth weight. PFAS may also impair fetal growth through endocrine effects. Estrogenic effects have been noted in in vivo and in vitro studies. Overall, data suggest thyroid-damaging effects of PFAS affecting thyroid hormones, thyroid hormone gene expression, and histology that are associated in animal studies with decreased body and organ weight. The effects of PFAS on the complex relationships between oxidative stress, endocrine system function, adipogenesis, and fetal growth should be further explored.
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Affiliation(s)
- Claudia Gundacker
- Institute of Medical Genetics, Medical University of Vienna, 1090 Vienna, Austria
- Correspondence: ; Tel.: +43-1-40160-56503
| | - Karine Audouze
- Unit T3S, Université Paris Cité, Inserm U1124, 75006 Paris, France
| | - Raimund Widhalm
- Institute of Medical Genetics, Medical University of Vienna, 1090 Vienna, Austria
| | - Sebastian Granitzer
- Institute of Medical Genetics, Medical University of Vienna, 1090 Vienna, Austria
| | - Martin Forsthuber
- Institute of Medical Genetics, Medical University of Vienna, 1090 Vienna, Austria
| | - Florence Jornod
- Unit T3S, Université Paris Cité, Inserm U1124, 75006 Paris, France
| | - Maria Wielsøe
- Department of Public Health, Aarhus University, 8000 Aarhus, Denmark
| | - Manhai Long
- Department of Public Health, Aarhus University, 8000 Aarhus, Denmark
| | - Thórhallur Ingi Halldórsson
- Faculty of Food Science and Nutrition, University of Iceland, 102 Reykjavík, Iceland
- Department of Epidemiology Research, Statens Serum Institut, 2300 Copenhagen, Denmark
| | - Maria Uhl
- Environment Agency Austria, 1090 Vienna, Austria
| | - Eva Cecilie Bonefeld-Jørgensen
- Department of Public Health, Aarhus University, 8000 Aarhus, Denmark
- Greenland Center for Health Research, Greenland University, Nuuk 3905, Greenland
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3
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Lv Y, Wang H, Li G, Zhao B. Three-dimensional decellularized tumor extracellular matrices with different stiffness as bioengineered tumor scaffolds. Bioact Mater 2021; 6:2767-2782. [PMID: 33665508 PMCID: PMC7897907 DOI: 10.1016/j.bioactmat.2021.02.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/25/2021] [Accepted: 02/05/2021] [Indexed: 02/07/2023] Open
Abstract
In the three-dimensional (3D) tumor microenvironment, matrix stiffness is associated with the regulation of tumor cells behaviors. In vitro tumor models with appropriate matrix stiffness are urgently desired. Herein, we prepare 3D decellularized extracellular matrix (DECM) scaffolds with different stiffness to mimic the microenvironment of human breast tumor tissue, especially the matrix stiffness, components and structure of ECM. Furthermore, the effects of matrix stiffness on the drug resistance of human breast cancer cells are explored with these developed scaffolds as case studies. Our results confirm that DECM scaffolds with diverse stiffness can be generated by tumor cells with different lysyl oxidase (LOX) expression levels, while the barely intact structure and major components of the ECM are maintained without cells. This versatile 3D tumor model with suitable stiffness can be used as a bioengineered tumor scaffold to investigate the role of the microenvironment in tumor progression and to screen drugs prior to clinical use to a certain extent. Novel 3D bioengineered tumor scaffolds with different stiffness were developed. Cells with different LOX expression levels were used to generate tumor tissue. DECM scaffold has good cytocompatibility. DECM with high stiffness promotes the resistance of MDA-MB-231 cells to cisplatin. DECM with high stiffness increases the expression of Bcl-2 and ABCB1.
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Affiliation(s)
- Yonggang Lv
- Mechanobiology and Regenerative Medicine Laboratory, Bioengineering College, Chongqing University, Chongqing, 400044, PR China.,Key Laboratory of Biorheological Science and Technology, Chongqing University, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400044, PR China
| | - Hongjun Wang
- Mechanobiology and Regenerative Medicine Laboratory, Bioengineering College, Chongqing University, Chongqing, 400044, PR China.,Key Laboratory of Biorheological Science and Technology, Chongqing University, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400044, PR China
| | - Gui Li
- Mechanobiology and Regenerative Medicine Laboratory, Bioengineering College, Chongqing University, Chongqing, 400044, PR China.,Key Laboratory of Biorheological Science and Technology, Chongqing University, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400044, PR China
| | - Boyuan Zhao
- Mechanobiology and Regenerative Medicine Laboratory, Bioengineering College, Chongqing University, Chongqing, 400044, PR China.,Key Laboratory of Biorheological Science and Technology, Chongqing University, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, 400044, PR China
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4
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Catozzi S, Halasz M, Kiel C. Predicted 'wiring landscape' of Ras-effector interactions in 29 human tissues. NPJ Syst Biol Appl 2021; 7:10. [PMID: 33580066 PMCID: PMC7881153 DOI: 10.1038/s41540-021-00170-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 10/19/2020] [Indexed: 02/07/2023] Open
Abstract
Ras is a plasma membrane (PM)-associated signaling hub protein that interacts with its partners (effectors) in a mutually exclusive fashion. We have shown earlier that competition for binding and hence the occurrence of specific binding events at a hub protein can modulate the activation of downstream pathways. Here, using a mechanistic modeling approach that incorporates high-quality proteomic data of Ras and 56 effectors in 29 (healthy) human tissues, we quantified the amount of individual Ras-effector complexes, and characterized the (stationary) Ras "wiring landscape" specific to each tissue. We identified nine effectors that are in significant amount in complex with Ras in at least one of the 29 tissues. We simulated both mutant- and stimulus-induced network re-configurations, and assessed their divergence from the reference scenario, specifically discussing a case study for two stimuli in three epithelial tissues. These analyses pointed to 32 effectors that are in significant amount in complex with Ras only if they are additionally recruited to the PM, e.g. via membrane-binding domains or domains binding to activated receptors at the PM. Altogether, our data emphasize the importance of tissue context for binding events at the Ras signaling hub.
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Affiliation(s)
- Simona Catozzi
- UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield, Dublin, 4, Ireland
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Melinda Halasz
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Christina Kiel
- UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield, Dublin, 4, Ireland.
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, Dublin, 4, Ireland.
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5
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Nielsen NS, Poulsen ET, Lukassen MV, Chao Shern C, Mogensen EH, Weberskov CE, DeDionisio L, Schauser L, Moore TC, Otzen DE, Hjortdal J, Enghild JJ. Biochemical mechanisms of aggregation in TGFBI-linked corneal dystrophies. Prog Retin Eye Res 2020; 77:100843. [DOI: 10.1016/j.preteyeres.2020.100843] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/17/2020] [Accepted: 01/23/2020] [Indexed: 12/22/2022]
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6
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Miyawaki H, Kioka H, Sato K, Kurashige M, Ozawa T, Shibayama H, Hikoso S, Morii E, Yamauchi-Takihara K, Sakata Y. Long-term Effects of the Janus Kinase 1/2 Inhibitor Ruxolitinib on Pulmonary Hypertension and the Cardiac Function in a Patient with Myelofibrosis. Intern Med 2020; 59:229-233. [PMID: 31534088 PMCID: PMC7008043 DOI: 10.2169/internalmedicine.3528-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Constitutive activation of the Janus kinase/signal transduction and activator of transcription (JAK-STAT) signaling pathway plays a central role in the pathogenesis of myelofibrosis (MF) and pulmonary hypertension (PH) is a known complication of MF. On the other hand, it has been proposed that the JAK-STAT pathway, especially signal transducer and activation of transcription (STAT) 3 activation, protects cardiomyocytes from various stresses. We describe the case of a patient with MF-associated PH who developed left ventricular dysfunction after five years of treatment with the JAK 1/2 inhibitor, ruxolitinib. This is the first report with histopathological findings that demonstrate possible contradictory effects of a JAK 1/2 inhibitor: improvement of MF-associated PH and cardiotoxicity.
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Affiliation(s)
- Hiroshi Miyawaki
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Japan
| | - Hidetaka Kioka
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Japan
| | - Kazuaki Sato
- Department of Pathology, Osaka University Graduate School of Medicine, Japan
| | - Masako Kurashige
- Department of Pathology, Osaka University Graduate School of Medicine, Japan
| | - Takayuki Ozawa
- Department of Hematology and Oncology, Osaka University Graduate School of Medicine, Japan
| | - Hirohiko Shibayama
- Department of Hematology and Oncology, Osaka University Graduate School of Medicine, Japan
| | - Shungo Hikoso
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Japan
| | - Eiichi Morii
- Department of Pathology, Osaka University Graduate School of Medicine, Japan
| | - Keiko Yamauchi-Takihara
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Japan
- Health Care Center, Osaka University, Japan
| | - Yasushi Sakata
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Japan
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7
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Baskar R, Fienberg HG, Khair Z, Favaro P, Kimmey S, Green DR, Nolan GP, Plevritis S, Bendall SC. TRAIL-induced variation of cell signaling states provides nonheritable resistance to apoptosis. Life Sci Alliance 2019; 2:e201900554. [PMID: 31704709 PMCID: PMC6848270 DOI: 10.26508/lsa.201900554] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/24/2019] [Accepted: 10/25/2019] [Indexed: 02/06/2023] Open
Abstract
TNFα-related apoptosis-inducing ligand (TRAIL), specifically initiates programmed cell death, but often fails to eradicate all cells, making it an ineffective therapy for cancer. This fractional killing is linked to cellular variation that bulk assays cannot capture. Here, we quantify the diversity in cellular signaling responses to TRAIL, linking it to apoptotic frequency across numerous cell systems with single-cell mass cytometry (CyTOF). Although all cells respond to TRAIL, a variable fraction persists without apoptotic progression. This cell-specific behavior is nonheritable where both the TRAIL-induced signaling responses and frequency of apoptotic resistance remain unaffected by prior exposure. The diversity of signaling states upon exposure is correlated to TRAIL resistance. Concomitantly, constricting the variation in signaling response with kinase inhibitors proportionally decreases TRAIL resistance. Simultaneously, TRAIL-induced de novo translation in resistant cells, when blocked by cycloheximide, abrogated all TRAIL resistance. This work highlights how cell signaling diversity, and subsequent translation response, relates to nonheritable fractional escape from TRAIL-induced apoptosis. This refined view of TRAIL resistance provides new avenues to study death ligands in general.
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Affiliation(s)
- Reema Baskar
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Harris G Fienberg
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Zumana Khair
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Patricia Favaro
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sam Kimmey
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Developmental Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Garry P Nolan
- Baxter Laboratory, Stanford University School of Medicine, Stanford, CA, USA
| | - Sylvia Plevritis
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Sean C Bendall
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
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8
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Wittkowski P, Marx-Stoelting P, Violet N, Fetz V, Schwarz F, Oelgeschläger M, Schönfelder G, Vogl S. Caenorhabditis elegans As a Promising Alternative Model for Environmental Chemical Mixture Effect Assessment-A Comparative Study. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:12725-12733. [PMID: 31536708 DOI: 10.1021/acs.est.9b03266] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
A key challenge of mixture toxicity testing is that a multitude of substances with even more combinations need to be tested in a broad dose range. Consequently testing in rodent bioassays, the current gold standard of toxicity testing, is hardly feasible. High-throughput compatible cell culture systems, however, suffer from limitations with respect to toxicokinetics, tissue interactions, and compensatory mechanisms. Therefore, simple organisms like the nematode Caenorhabditis elegans, combining relevant advantages of complex in vivo and fast in vitro assays might prove highly valuable within a testing strategy for mixtures. To investigate the comparability between results obtained with C. elegans and traditional rodent assays, we used five azole fungicides as well investigated model substances. Our findings suggest that azoles act additively in C. elegans which is in line with previous results in rats. Additionally, we show that toxicokinetics are one important factor for the differences in the relative toxicity of the azoles in both species. Importantly, we also demonstrate that in contrast to most rodent in vivo studies, C. elegans assays provide well-defined concentration-response relationships which are a very good basis for the prediction of mixture effects. We conclude that C. elegans may be an appropriate model for mixture toxicity testing at least within a first step to identify and prioritize relevant mixtures for further testing.
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Affiliation(s)
- Paul Wittkowski
- German Federal Institute for Risk Assessment , German Centre for the Protection of Laboratory Animals (Bf3R) , 10589 Berlin , Germany
| | - Philip Marx-Stoelting
- German Federal Institute for Risk Assessment , German Centre for the Protection of Laboratory Animals (Bf3R) , 10589 Berlin , Germany
| | - Norman Violet
- German Federal Institute for Risk Assessment , German Centre for the Protection of Laboratory Animals (Bf3R) , 10589 Berlin , Germany
| | - Verena Fetz
- German Federal Institute for Risk Assessment , German Centre for the Protection of Laboratory Animals (Bf3R) , 10589 Berlin , Germany
| | - Franziska Schwarz
- German Federal Institute for Risk Assessment , German Centre for the Protection of Laboratory Animals (Bf3R) , 10589 Berlin , Germany
| | - Michael Oelgeschläger
- German Federal Institute for Risk Assessment , German Centre for the Protection of Laboratory Animals (Bf3R) , 10589 Berlin , Germany
| | - Gilbert Schönfelder
- German Federal Institute for Risk Assessment , German Centre for the Protection of Laboratory Animals (Bf3R) , 10589 Berlin , Germany
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin , Humboldt-Universität zu Berlin, and Berlin Institute of Health , 10117 Berlin , Germany
| | - Silvia Vogl
- German Federal Institute for Risk Assessment , German Centre for the Protection of Laboratory Animals (Bf3R) , 10589 Berlin , Germany
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9
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George J, Hsu CC, Nguyen LTB, Ye H, Cui Z. Neural tissue engineering with structured hydrogels in CNS models and therapies. Biotechnol Adv 2019; 42:107370. [PMID: 30902729 DOI: 10.1016/j.biotechadv.2019.03.009] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 02/25/2019] [Accepted: 03/11/2019] [Indexed: 01/27/2023]
Abstract
The development of techniques to create and use multiphase microstructured hydrogels (granular hydrogels or microgels) has enabled the generation of cultures with more biologically relevant architecture and use of structured hydrogels is especially pertinent to the development of new types of central nervous system (CNS) culture models and therapies. We review material choice and the customisation of hydrogel structure, as well as the use of hydrogels in developmental models. Combining the use of structured hydrogel techniques with developmentally relevant tissue culture approaches will enable the generation of more relevant models and treatments to repair damaged CNS tissue architecture.
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Affiliation(s)
- Julian George
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, United Kingdom
| | - Chia-Chen Hsu
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, United Kingdom
| | - Linh Thuy Ba Nguyen
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, United Kingdom
| | - Hua Ye
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, United Kingdom.
| | - Zhanfeng Cui
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, United Kingdom.
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10
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Zapata L, Pich O, Serrano L, Kondrashov FA, Ossowski S, Schaefer MH. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biol 2018; 19:67. [PMID: 29855388 PMCID: PMC5984361 DOI: 10.1186/s13059-018-1434-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 04/20/2018] [Indexed: 01/08/2023] Open
Abstract
Background Natural selection shapes cancer genomes. Previous studies used signatures of positive selection to identify genes driving malignant transformation. However, the contribution of negative selection against somatic mutations that affect essential tumor functions or specific domains remains a controversial topic. Results Here, we analyze 7546 individual exomes from 26 tumor types from TCGA data to explore the portion of the cancer exome under negative selection. Although we find most of the genes neutrally evolving in a pan-cancer framework, we identify essential cancer genes and immune-exposed protein regions under significant negative selection. Moreover, our simulations suggest that the amount of negative selection is underestimated. We therefore choose an empirical approach to identify genes, functions, and protein regions under negative selection. We find that expression and mutation status of negatively selected genes is indicative of patient survival. Processes that are most strongly conserved are those that play fundamental cellular roles such as protein synthesis, glucose metabolism, and molecular transport. Intriguingly, we observe strong signals of selection in the immunopeptidome and proteins controlling peptide exposition, highlighting the importance of immune surveillance evasion. Additionally, tumor type-specific immune activity correlates with the strength of negative selection on human epitopes. Conclusions In summary, our results show that negative selection is a hallmark of cell essentiality and immune response in cancer. The functional domains identified could be exploited therapeutically, ultimately allowing for the development of novel cancer treatments. Electronic supplementary material The online version of this article (10.1186/s13059-018-1434-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luis Zapata
- Genomic and Epigenomic Variation in Disease Group, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.,Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Oriol Pich
- Evolutionary Genomics Group, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain
| | - Luis Serrano
- Design of Biological Systems Group, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys 23, 08010, Barcelona, Spain
| | - Fyodor A Kondrashov
- IST Austria (Institute of Science and Technology Austria), Am Campus 1, 3400, Klosterneuburg, Austria
| | - Stephan Ossowski
- Genomic and Epigenomic Variation in Disease Group, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain. .,Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.
| | - Martin H Schaefer
- Design of Biological Systems Group, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.
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11
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Bergan-Roller HE, Sheridan MA. The growth hormone signaling system: Insights into coordinating the anabolic and catabolic actions of growth hormone. Gen Comp Endocrinol 2018; 258:119-133. [PMID: 28760716 DOI: 10.1016/j.ygcen.2017.07.028] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 07/19/2017] [Accepted: 07/27/2017] [Indexed: 12/16/2022]
Abstract
Although growth hormone (GH) is a multifunctional factor that coordinates various aspects of feeding, reproduction, osmoregulation, and immune system function, perhaps two of its most studied actions are the regulation of growth and metabolism, particularly lipid metabolism. In this review, we describe the major growth-promoting and lipid metabolic actions of GH and then discuss how the GH system regulates these actions. Numerous intrinsic and extrinsic factors provide information about the metabolic status of the organism and influence the production of release of GH. The actions of GH are mediated by GH receptors (GHR), which are widely distributed among tissues. Teleosts possess multiple forms of GHRs that arose through the evolution of this group. Modulation of tissue responsiveness to GH is regulated by molecular and functional expression of GHRs, and in teleosts GHR subtypes, by various factors that reflect the metabolic and growth status of the organism, including nutritional state. The action of GH is propagated by the linkage of GHRs to several cellular effector systems, including JAK-STAT, ERK, PI3K-Akt, and PKC. The differential activation of these pathways, which is governed by nutrient status, underlies GH stimulation of growth or GH stimulation of lipolysis. Taken together, the multi-functional actions of GH are determined by the distribution and abundance of GHRs (and GHR subtypes in teleosts) as well as by the GHR-effector system linkages.
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Affiliation(s)
| | - Mark A Sheridan
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409 USA.
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12
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Pérez-Sánchez J, Simó-Mirabet P, Naya-Català F, Martos-Sitcha JA, Perera E, Bermejo-Nogales A, Benedito-Palos L, Calduch-Giner JA. Somatotropic Axis Regulation Unravels the Differential Effects of Nutritional and Environmental Factors in Growth Performance of Marine Farmed Fishes. Front Endocrinol (Lausanne) 2018; 9:687. [PMID: 30538673 PMCID: PMC6277588 DOI: 10.3389/fendo.2018.00687] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 11/02/2018] [Indexed: 12/23/2022] Open
Abstract
The Gh/Prl/Sl family has evolved differentially through evolution, resulting in varying relationships between the somatotropic axis and growth rates within and across fish species. This is due to a wide range of endogenous and exogenous factors that make this association variable throughout season and life cycle, and the present minireview aims to better define the nutritional and environmental regulation of the endocrine growth cascade over precisely defined groups of fishes, focusing on Mediterranean farmed fishes. As a result, circulating Gh and Igf-i are revitalized as reliable growth markers, with a close association with growth rates of gilthead sea bream juveniles with deficiency signs in both macro- or micro-nutrients. This, together with other regulated responses, promotes the use of Gh and Igf-i as key performance indicators of growth, aerobic scope, and nutritional condition in gilthead sea bream. Moreover, the sirtuin-energy sensors might modulate the growth-promoting action of somatotropic axis. In this scenario, transcripts of igf-i and gh receptors mirror changes in plasma Gh and Igf-i levels, with the ghr-i/ghr-ii expression ratio mostly unaltered over season. However, this ratio is nutritionally regulated, and enriched plant-based diets or diets with specific nutrient deficiencies downregulate hepatic ghr-i, decreasing the ghr-i/ghr-ii ratio. The same trend, due to a ghr-ii increase, is found in skeletal muscle, whereas impaired growth during overwintering is related to increase in the ghr-i/ghr-ii and igf-ii/igf-i ratios in liver and skeletal muscle, respectively. Overall, expression of insulin receptors and igf receptors is less regulated, though the expression quotient is especially high in the liver and muscle of sea bream. Nutritional and environmental regulation of the full Igf binding protein 1-6 repertoire remains to be understood. However, tissue-specific expression profiling highlights an enhanced and nutritionally regulated expression of the igfbp-1/-2/-4 clade in liver, whereas the igfbp-3/-5/-6 clade is overexpressed and regulated in skeletal muscle. The somatotropic axis is, therefore, highly informative of a wide-range of growth-disturbing and stressful stimuli, and multivariate analysis supports its use as a reliable toolset for the assessment of growth potentiality and nutrient deficiencies and requirements, especially in combination with selected panels of other nutritionally regulated metabolic biomarkers.
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Abstract
How can we treat cancer more effectively? Traditionally, tumours from the same anatomical site are treated as one tumour entity. This concept has been challenged by recent breakthroughs in cancer genomics and translational research that have enabled molecular tumour profiling. The identification and validation of cancer drivers that are shared between different tumour types, spurred the new paradigm to target driver pathways across anatomical sites by off-label drug use, or within so-called basket or umbrella trials which are designed to test whether molecular alterations in one tumour entity can be extrapolated to all others. However, recent clinical and preclinical studies suggest that there are tissue- and cell type-specific differences in tumorigenesis and the organization of oncogenic signalling pathways. In this Opinion article, we focus on the molecular, cellular, systemic and environmental determinants of organ-specific tumorigenesis and the mechanisms of context-specific oncogenic signalling outputs. Investigation, recognition and in-depth biological understanding of these differences will be vital for the design of next-generation clinical trials and the implementation of molecularly guided cancer therapies in the future.
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Affiliation(s)
- Günter Schneider
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Ismaningerstr. 22, 81675 München, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Marc Schmidt-Supprian
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- Department of Medicine III, Klinikum rechts der Isar, Technische Universität München, Ismaningerstr. 22, 81675 München, Germany
| | - Roland Rad
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Ismaningerstr. 22, 81675 München, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Dieter Saur
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Ismaningerstr. 22, 81675 München, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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14
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Alanis-Lobato G, Andrade-Navarro MA, Schaefer MH. HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks. Nucleic Acids Res 2016; 45:D408-D414. [PMID: 27794551 PMCID: PMC5210659 DOI: 10.1093/nar/gkw985] [Citation(s) in RCA: 280] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 09/28/2016] [Accepted: 10/14/2016] [Indexed: 01/01/2023] Open
Abstract
The increasing number of experimentally detected interactions between proteins makes it difficult for researchers to extract the interactions relevant for specific biological processes or diseases. This makes it necessary to accompany the large-scale detection of protein–protein interactions (PPIs) with strategies and tools to generate meaningful PPI subnetworks. To this end, we generated the Human Integrated Protein–Protein Interaction rEference or HIPPIE (http://cbdm.uni-mainz.de/hippie/). HIPPIE is a one-stop resource for the generation and interpretation of PPI networks relevant to a specific research question. We provide means to generate highly reliable, context-specific PPI networks and to make sense out of them. We just released the second major update of HIPPIE, implementing various new features. HIPPIE grew substantially over the last years and now contains more than 270 000 confidence scored and annotated PPIs. We integrated different types of experimental information for the confidence scoring and the construction of context-specific networks. We implemented basic graph algorithms that highlight important proteins and interactions. HIPPIE's graphical interface implements several ways for wet lab and computational scientists alike to access the PPI data.
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Affiliation(s)
- Gregorio Alanis-Lobato
- Faculty of Biology, Johannes Gutenberg Universität, Mainz, Germany
- Institute of Molecular Biology, Mainz, Germany
| | - Miguel A Andrade-Navarro
- Faculty of Biology, Johannes Gutenberg Universität, Mainz, Germany
- Institute of Molecular Biology, Mainz, Germany
| | - Martin H Schaefer
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
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15
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Identifying clinically relevant drug resistance genes in drug-induced resistant cancer cell lines and post-chemotherapy tissues. Oncotarget 2016; 6:41216-27. [PMID: 26515599 PMCID: PMC4747401 DOI: 10.18632/oncotarget.5649] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 09/12/2015] [Indexed: 12/13/2022] Open
Abstract
Until recently, few molecular signatures of drug resistance identified in drug-induced resistant cancer cell models can be translated into clinical practice. Here, we defined differentially expressed genes (DEGs) between pre-chemotherapy colorectal cancer (CRC) tissue samples of non-responders and responders for 5-fluorouracil and oxaliplatin-based therapy as clinically relevant drug resistance genes (CRG5-FU/L-OHP). Taking CRG5-FU/L-OHP as reference, we evaluated the clinical relevance of several types of genes derived from HCT116 CRC cells with resistance to 5-fluorouracil and oxaliplatin, respectively. The results revealed that DEGs between parental and resistant cells, when both were treated with the corresponding drug for a certain time, were significantly consistent with the CRG5-FU/L-OHP as well as the DEGs between the post-chemotherapy CRC specimens of responders and non-responders. This study suggests a novel strategy to extract clinically relevant drug resistance genes from both drug-induced resistant cell models and post-chemotherapy cancer tissue specimens.
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16
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Gordon NK, Gordon R. The organelle of differentiation in embryos: the cell state splitter. Theor Biol Med Model 2016; 13:11. [PMID: 26965444 PMCID: PMC4785624 DOI: 10.1186/s12976-016-0037-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/27/2016] [Indexed: 12/16/2022] Open
Abstract
The cell state splitter is a membraneless organelle at the apical end of each epithelial cell in a developing embryo. It consists of a microfilament ring and an intermediate filament ring subtending a microtubule mat. The microtubules and microfilament ring are in mechanical opposition as in a tensegrity structure. The cell state splitter is bistable, perturbations causing it to contract or expand radially. The intermediate filament ring provides metastability against small perturbations. Once this snap-through organelle is triggered, it initiates signal transduction to the nucleus, which changes gene expression in one of two readied manners, causing its cell to undergo a step of determination and subsequent differentiation. The cell state splitter also triggers the cell state splitters of adjacent cells to respond, resulting in a differentiation wave. Embryogenesis may be represented then as a bifurcating differentiation tree, each edge representing one cell type. In combination with the differentiation waves they propagate, cell state splitters explain the spatiotemporal course of differentiation in the developing embryo. This review is excerpted from and elaborates on "Embryogenesis Explained" (World Scientific Publishing, Singapore, 2016).
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Affiliation(s)
| | - Richard Gordon
- />Retired, University of Manitoba, Winnipeg, Canada
- />Embryogenesis Center, Gulf Specimen Aquarium & Marine Laboratory, 222 Clark Drive, Panacea, FL 32346 USA
- />C.S. Mott Center for Human Growth & Development, Department of Obstetrics & Gynecology, Wayne State University, 275 E. Hancock, Detroit, MI 48201 USA
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17
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Schaefer MH, Serrano L. Cell type-specific properties and environment shape tissue specificity of cancer genes. Sci Rep 2016; 6:20707. [PMID: 26856619 PMCID: PMC4746590 DOI: 10.1038/srep20707] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/11/2016] [Indexed: 12/21/2022] Open
Abstract
One of the biggest mysteries in cancer research remains why mutations in certain genes cause cancer only at specific sites in the human body. The poor correlation between the expression level of a cancer gene and the tissues in which it causes malignant transformations raises the question of which factors determine the tissue-specific effects of a mutation. Here, we explore why some cancer genes are associated only with few different cancer types (i.e., are specific), while others are found mutated in a large number of different types of cancer (i.e., are general). We do so by contrasting cellular functions of specific-cancer genes with those of general ones to identify properties that determine where in the body a gene mutation is causing malignant transformations. We identified different groups of cancer genes that did not behave as expected (i.e., DNA repair genes being tissue specific, immune response genes showing a bimodal specificity function or strong association of generally expressed genes to particular cancers). Analysis of these three groups demonstrates the importance of environmental impact for understanding why certain cancer genes are only involved in the development of some cancer types but are rarely found mutated in other types of cancer.
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Affiliation(s)
- Martin H Schaefer
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, Barcelona, Spain
| | - Luis Serrano
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, Barcelona, Spain
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18
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Beltran-Sastre V, Benisty H, Burnier J, Berger I, Serrano L, Kiel C. Tuneable endogenous mammalian target complementation via multiplexed plasmid-based recombineering. Sci Rep 2015; 5:17432. [PMID: 26612112 PMCID: PMC4661934 DOI: 10.1038/srep17432] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 10/29/2015] [Indexed: 12/26/2022] Open
Abstract
Understanding the quantitative functional consequences of human disease mutations requires silencing of endogenous genes and expression of mutants at close to physiological levels. Changing protein levels above or below these levels is also important for system perturbation and modelling. Fast design optimization demands flexible interchangeable cassettes for endogenous gene silencing and tuneable expression. Here, we introduce ‘TEMTAC’, a multigene recombineering and delivery system for simultaneous siRNA-based knockdown and regulated mutant (or other variant) expression with different dynamic ranges. We show its applicability by confirming known phenotypic effects for selected mutations for BRAF, HRAS, and SHP2.
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Affiliation(s)
- Violeta Beltran-Sastre
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Hannah Benisty
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Julia Burnier
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Imre Berger
- European Molecular Biology Laboratory, Grenoble Outstation, B.P. 181, Grenoble, France.,The School of Biochemistry, University of Bristol, Clifton BS8 1TD, United Kingdom
| | - Luis Serrano
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Christina Kiel
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
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Ao L, Yan H, Zheng T, Wang H, Tong M, Guan Q, Li X, Cai H, Li M, Guo Z. Identification of reproducible drug-resistance-related dysregulated genes in small-scale cancer cell line experiments. Sci Rep 2015; 5:11895. [PMID: 26173481 PMCID: PMC4502408 DOI: 10.1038/srep11895] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 06/09/2015] [Indexed: 11/25/2022] Open
Abstract
Researchers usually measure only a few technical replicates of two types of cell line, resistant or sensitive to a drug, and use a fold-change (FC) cut-off value to detect differentially expressed (DE) genes. However, the FC cut-off lacks statistical control and is biased towards the identification of genes with low expression levels in both cell lines. Here, viewing every pair of resistant-sensitive technical replicates as an experiment, we proposed an algorithm to identify DE genes by evaluating the reproducibility of the expression difference or FC between every two independent experiments without overlapping samples. Using four small datasets of cancer cell line resistant or sensitive to a drug, we demonstrated that this algorithm could efficiently capture reproducible DE genes significantly enriched in biological pathways relevant to the corresponding drugs, whereas many of them could not be found by the FC and other commonly used methods. Therefore, the proposed algorithm is an effective complement to current approaches for analysing small cancer cell line data.
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Affiliation(s)
- Lu Ao
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350108
| | - Haidan Yan
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350108
| | | | - Hongwei Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150001
| | - Mengsha Tong
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350108
| | - Qingzhou Guan
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350108
| | - Xiangyu Li
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350108
| | - Hao Cai
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350108
| | - Mengyao Li
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350108
| | - Zheng Guo
- 1] Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350108 [2] College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150001
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20
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Toufighi K, Yang JS, Luis NM, Aznar Benitah S, Lehner B, Serrano L, Kiel C. Dissecting the calcium-induced differentiation of human primary keratinocytes stem cells by integrative and structural network analyses. PLoS Comput Biol 2015; 11:e1004256. [PMID: 25946651 PMCID: PMC4422705 DOI: 10.1371/journal.pcbi.1004256] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 03/25/2015] [Indexed: 12/19/2022] Open
Abstract
The molecular details underlying the time-dependent assembly of protein complexes in cellular networks, such as those that occur during differentiation, are largely unexplored. Focusing on the calcium-induced differentiation of primary human keratinocytes as a model system for a major cellular reorganization process, we look at the expression of genes whose products are involved in manually-annotated protein complexes. Clustering analyses revealed only moderate co-expression of functionally related proteins during differentiation. However, when we looked at protein complexes, we found that the majority (55%) are composed of non-dynamic and dynamic gene products ('di-chromatic'), 19% are non-dynamic, and 26% only dynamic. Considering three-dimensional protein structures to predict steric interactions, we found that proteins encoded by dynamic genes frequently interact with a common non-dynamic protein in a mutually exclusive fashion. This suggests that during differentiation, complex assemblies may also change through variation in the abundance of proteins that compete for binding to common proteins as found in some cases for paralogous proteins. Considering the example of the TNF-α/NFκB signaling complex, we suggest that the same core complex can guide signals into diverse context-specific outputs by addition of time specific expressed subunits, while keeping other cellular functions constant. Thus, our analysis provides evidence that complex assembly with stable core components and competition could contribute to cell differentiation.
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Affiliation(s)
- Kiana Toufighi
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Jae-Seong Yang
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Nuno Miguel Luis
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Salvador Aznar Benitah
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Institute for Research in Biomedicine, Parc Científic de Barcelona, Barcelona, Spain
- * E-mail: (SAB); (BL); (LS); (CK)
| | - Ben Lehner
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- * E-mail: (SAB); (BL); (LS); (CK)
| | - Luis Serrano
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- * E-mail: (SAB); (BL); (LS); (CK)
| | - Christina Kiel
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- * E-mail: (SAB); (BL); (LS); (CK)
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Kianianmomeni A. Cell-type specific photoreceptors and light signaling pathways in the multicellular green alga Volvox carteri and their potential role in cellular differentiation. PLANT SIGNALING & BEHAVIOR 2015; 10:e1010935. [PMID: 25874475 PMCID: PMC4623044 DOI: 10.1080/15592324.2015.1010935] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 12/26/2014] [Accepted: 01/05/2015] [Indexed: 06/04/2023]
Abstract
The formation of multicellular organisms requires genetically predefined signaling pathways in various cell types. Besides differences in size, energy balance and life time, cell types should be enable to modulate appropriate developmental and adaptive responses in ever-changing surrounding environment. One of the most important environmental cues is light which regulates a variety of physiological and cellular processes. During evolution, diverse light-sensitive proteins, so-called photoreceptors, and corresponding signaling pathways have evolved, in almost all kingdoms of life, to monitor light continuously and adjust their growth and development accordingly. However, considering the fact that different cell types should be enable to trigger distinct light signaling pathways according to their needs, cell-type specific light signaling pathways are required to guarantee cell type-matched modulation of cellular and developmental processes in response to different light signals. The multicellular green alga Volvox carteri, which has only 2 cell types with clear division of labor, possesses cell-type specific photoreceptors and light signaling pathways which allow differential regulation of genes involved in various cellular and metabolic pathways in response to environmental light. The existence of cell-type specific light signaling pathways in multicellular organism like Volvox reflects an early development of cell-type specific signaling mechanisms during evolution to ensure maintenance of differentiation.
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Affiliation(s)
- Arash Kianianmomeni
- Department of Cellular and Developmental Biology of Plants; University of Bielefeld; Bielefeld, Germany
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