1
|
Balasubramanian S, Perumal E. Integrated in silico analysis of transcriptomic alterations in nanoparticle toxicity across human and mouse models. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:174897. [PMID: 39053559 DOI: 10.1016/j.scitotenv.2024.174897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/17/2024] [Accepted: 07/17/2024] [Indexed: 07/27/2024]
Abstract
Nanoparticles, due to their exceptional physicochemical properties are used in our day-to-day environment. They are currently not regulated which might lead to increased levels in the biological systems causing adverse effects. However, the overall mechanism behind nanotoxicity remains elusive. Previously, we analysed the transcriptome datasets of copper oxide nanoparticles using in silico tools and identified IL-17, chemokine signaling pathway, and cytokine-cytokine receptor interaction as the key pathways altered. Based on the findings, we hypothesized a common pathway could be involved in transition metal oxide nanoparticles toxicity irrespective of the variables. Further, there could be unique transcriptome changes between metal oxide nanoparticles and other nanoparticles. To accomplish this, the overall transcriptome datasets of nanoparticles consisting of microarray and RNA-Seq were obtained. >90 studies for 17 different nanoparticles, performed in humans, rats, and mice were assessed. After initial screening, 24 mouse studies (with 196 datasets) and 34 human studies (with 200 datasets) were used for further analyses. The common genes that are dysregulated upon NPs exposure were identified for human and mouse datasets separately. Further, an overrepresentation functional enrichment analysis was performed. The common genes, their gene ontology, gene-gene, and protein-protein interactions were assessed. The overall results suggest that IL-17 and its related pathways might be commonly altered in nanoparticle exposure with lung as one of the major organs affected.
Collapse
Affiliation(s)
- Satheeswaran Balasubramanian
- Molecular Toxicology Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu 641046, India
| | - Ekambaram Perumal
- Molecular Toxicology Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu 641046, India.
| |
Collapse
|
2
|
Nguyen NHA, Falagan-Lotsch P. Mechanistic Insights into the Biological Effects of Engineered Nanomaterials: A Focus on Gold Nanoparticles. Int J Mol Sci 2023; 24:4109. [PMID: 36835521 PMCID: PMC9963226 DOI: 10.3390/ijms24044109] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 02/10/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Nanotechnology has great potential to significantly advance the biomedical field for the benefit of human health. However, the limited understanding of nano-bio interactions leading to unknowns about the potential adverse health effects of engineered nanomaterials and to the poor efficacy of nanomedicines has hindered their use and commercialization. This is well evidenced considering gold nanoparticles, one of the most promising nanomaterials for biomedical applications. Thus, a fundamental understanding of nano-bio interactions is of interest to nanotoxicology and nanomedicine, enabling the development of safe-by-design nanomaterials and improving the efficacy of nanomedicines. In this review, we introduce the advanced approaches currently applied in nano-bio interaction studies-omics and systems toxicology-to provide insights into the biological effects of nanomaterials at the molecular level. We highlight the use of omics and systems toxicology studies focusing on the assessment of the mechanisms underlying the in vitro biological responses to gold nanoparticles. First, the great potential of gold-based nanoplatforms to improve healthcare along with the main challenges for their clinical translation are presented. We then discuss the current limitations in the translation of omics data to support risk assessment of engineered nanomaterials.
Collapse
Affiliation(s)
- Nhung H. A. Nguyen
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec (TUL), Studentsk. 2, 46117 Liberec, Czech Republic
| | - Priscila Falagan-Lotsch
- Department of Biological Sciences, College of Sciences and Mathematics, Auburn University, Auburn, AL 36849, USA
| |
Collapse
|
3
|
Rodrigues JFV, de Souza GAP, Abrahão JS, Amaral RP, de Castro RFG, Malaquias LCC, Coelho LFL. Integrative transcriptome analysis of human cells treated with silver nanoparticles reveals a distinct cellular response and the importance of inorganic elements detoxification pathways. Biochim Biophys Acta Gen Subj 2022; 1866:130116. [DOI: 10.1016/j.bbagen.2022.130116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/28/2022] [Accepted: 02/21/2022] [Indexed: 01/01/2023]
|
4
|
Hafez AA, Salimi A, Jamali Z, Shabani M, Sheikhghaderi H. Overview of the application of inorganic nanomaterials in breast cancer diagnosis. INORG NANO-MET CHEM 2022. [DOI: 10.1080/24701556.2021.2025085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Asghar Ashrafi Hafez
- Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ahmad Salimi
- Department of Pharmacology and Toxicology, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
- Traditional Medicine and Hydrotherapy Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Zhaleh Jamali
- Student Research Committee, School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran
| | - Mohammad Shabani
- Student Research Committee, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Hiva Sheikhghaderi
- Student Research Committee, School of Paramedical, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Bukan Shahid Gholipour Hospital, Urmia University of Medical Sciences, Bukan, Iran
| |
Collapse
|
5
|
Chakraborty S, Gourain V, Benz M, Scheiger J, Levkin P, Popova A. Droplet microarrays for cell culture: effect of surface properties and nanoliter culture volume on global transcriptomic landscape. Mater Today Bio 2021; 11:100112. [PMID: 34124640 PMCID: PMC8175407 DOI: 10.1016/j.mtbio.2021.100112] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/09/2021] [Accepted: 04/13/2021] [Indexed: 11/20/2022] Open
Abstract
The development of novel chemically developed and physically defined surfaces and environments for cell culture and screening is important for various biological applications. The Droplet microarray (DMA) platform based on hydrophilic-superhydrophobic patterning enables high-throughput cellular screening in nanoliter volumes and on various biocompatible surfaces. Here we performed phenotypic and transcriptomic analysis of HeLa-CCL2 cells cultured on DMA, with a goal to analyze cellular response on different surfaces and culture volumes down to 3 nL, compared with conventional cell culture platforms. Our results indicate that cells cultured on four tested substrates: nanostructured nonpolymer, rough and smooth variants of poly(2-hydroxyethyl methacrylate-co-ethylene dimethacrylate) polymer and poly(thioether) dendrimer are compatible with cells grown in Petri dish. Cells cultured on nanostructured nonpolymer coating exhibited the closet transcriptomic resemblance to that of cells grown in Petri dish. Analysis of cells cultured in 100, 9, and 3 nL media droplets on DMA indicated that all but cells grown in 3 nL volumes had unperturbed viability with minimal alterations in the transcriptome compared with 96-well plate. Our findings demonstrate the applicability of DMA for cell-based assays and highlight the possibility of establishing regular cell culture on various biomaterial-coated substrates and in nanoliter volumes, along with routinely used cell culture platforms.
Collapse
Affiliation(s)
- S. Chakraborty
- Institute of Biological and Chemical Systems–Functional Molecular Systems (IBCS–FMS), Karlsruhe Institute of Technology (KIT), Hermann–von–Helmholtz–Platz 1, 76344 Eggenstein–Leopoldshafen, Germany
| | - V. Gourain
- Institute of Biological and Chemical Systems–Biological Information Processing (IBCS–BIP), Karlsruhe Institute of Technology (KIT), Hermann–von–Helmholtz–Platz 1, 76344 Eggenstein–Leopoldshafen, Germany
| | - M. Benz
- Institute of Biological and Chemical Systems–Functional Molecular Systems (IBCS–FMS), Karlsruhe Institute of Technology (KIT), Hermann–von–Helmholtz–Platz 1, 76344 Eggenstein–Leopoldshafen, Germany
| | - J.M. Scheiger
- Institute of Biological and Chemical Systems–Functional Molecular Systems (IBCS–FMS), Karlsruhe Institute of Technology (KIT), Hermann–von–Helmholtz–Platz 1, 76344 Eggenstein–Leopoldshafen, Germany
- Institute of Chemical Technology and Polymer Chemistry, Karlsruhe Institute of Technology (KIT), Engesserstr. 20, 76131 Karlsruhe, Germany
| | - P.A. Levkin
- Institute of Biological and Chemical Systems–Functional Molecular Systems (IBCS–FMS), Karlsruhe Institute of Technology (KIT), Hermann–von–Helmholtz–Platz 1, 76344 Eggenstein–Leopoldshafen, Germany
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber Weg 6, 76131 Karlsruhe, Germany
| | - A.A. Popova
- Institute of Biological and Chemical Systems–Functional Molecular Systems (IBCS–FMS), Karlsruhe Institute of Technology (KIT), Hermann–von–Helmholtz–Platz 1, 76344 Eggenstein–Leopoldshafen, Germany
| |
Collapse
|
6
|
Gallud A, Delaval M, Kinaret P, Marwah VS, Fortino V, Ytterberg J, Zubarev R, Skoog T, Kere J, Correia M, Loeschner K, Al‐Ahmady Z, Kostarelos K, Ruiz J, Astruc D, Monopoli M, Handy R, Moya S, Savolainen K, Alenius H, Greco D, Fadeel B. Multiparametric Profiling of Engineered Nanomaterials: Unmasking the Surface Coating Effect. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2002221. [PMID: 33240770 PMCID: PMC7675037 DOI: 10.1002/advs.202002221] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/29/2020] [Indexed: 05/02/2023]
Abstract
Despite considerable efforts, the properties that drive the cytotoxicity of engineered nanomaterials (ENMs) remain poorly understood. Here, the authors inverstigate a panel of 31 ENMs with different core chemistries and a variety of surface modifications using conventional in vitro assays coupled with omics-based approaches. Cytotoxicity screening and multiplex-based cytokine profiling reveals a good concordance between primary human monocyte-derived macrophages and the human monocyte-like cell line THP-1. Proteomics analysis following a low-dose exposure of cells suggests a nonspecific stress response to ENMs, while microarray-based profiling reveals significant changes in gene expression as a function of both surface modification and core chemistry. Pathway analysis highlights that the ENMs with cationic surfaces that are shown to elicit cytotoxicity downregulated DNA replication and cell cycle responses, while inflammatory responses are upregulated. These findings are validated using cell-based assays. Notably, certain small, PEGylated ENMs are found to be noncytotoxic yet they induce transcriptional responses reminiscent of viruses. In sum, using a multiparametric approach, it is shown that surface chemistry is a key determinant of cellular responses to ENMs. The data also reveal that cytotoxicity, determined by conventional in vitro assays, does not necessarily correlate with transcriptional effects of ENMs.
Collapse
Affiliation(s)
- Audrey Gallud
- Institute of Environmental MedicineKarolinska InstitutetStockholm171 77Sweden
| | - Mathilde Delaval
- Institute of Environmental MedicineKarolinska InstitutetStockholm171 77Sweden
| | - Pia Kinaret
- Faculty of Medicine and Health TechnologyTampere UniversityTampere33720Finland
- Institute of BiotechnologyUniversity of HelsinkiHelsinki00790Finland
| | - Veer Singh Marwah
- Faculty of Medicine and Health TechnologyTampere UniversityTampere33720Finland
- Institute of BiotechnologyUniversity of HelsinkiHelsinki00790Finland
| | - Vittorio Fortino
- Institute of BiomedicineUniversity of Eastern FinlandKuopio70211Finland
| | - Jimmy Ytterberg
- Department of Medical Biochemistry & BiophysicsKarolinska InstitutetStockholm171 77Sweden
| | - Roman Zubarev
- Department of Medical Biochemistry & BiophysicsKarolinska InstitutetStockholm171 77Sweden
| | - Tiina Skoog
- Department of Biosciences & NutritionKarolinska InstitutetHuddinge141 83Sweden
| | - Juha Kere
- Department of Biosciences & NutritionKarolinska InstitutetHuddinge141 83Sweden
| | - Manuel Correia
- National Food InstituteTechnical University of DenmarkKongens Lyngby2800Denmark
| | - Katrin Loeschner
- National Food InstituteTechnical University of DenmarkKongens Lyngby2800Denmark
| | - Zahraa Al‐Ahmady
- Faculty of BiologyMedicine & HealthUniversity of ManchesterManchesterM20 4GJUK
- School of Science & TechnologyNottingham Trent UniversityNottinghamNG1 8NSUK
| | - Kostas Kostarelos
- Faculty of BiologyMedicine & HealthUniversity of ManchesterManchesterM20 4GJUK
- Catalan Institute of Nanoscience and Nanotechnology (ICN2)Barcelona08193Spain
| | - Jaime Ruiz
- ISMUMR CNRS No. 5255University of BordeauxTalence33 405France
| | - Didier Astruc
- ISMUMR CNRS No. 5255University of BordeauxTalence33 405France
| | - Marco Monopoli
- Department of Pharmaceutical & Medicinal ChemistryRoyal College of Surgeons in Ireland (RCSI)Dublin2Ireland
| | - Richard Handy
- School of Biological & Marine SciencesUniversity of PlymouthPlymouthPL4 8AAUK
| | - Sergio Moya
- Soft Matter Nanotechnology LaboratoryCIC biomaGUNEDonostia‐San Sebastián20014Spain
| | - Kai Savolainen
- Finnish Institute of Occupational HealthHelsinki00032Finland
| | - Harri Alenius
- Institute of Environmental MedicineKarolinska InstitutetStockholm171 77Sweden
- Institute of BiotechnologyUniversity of HelsinkiHelsinki00790Finland
| | - Dario Greco
- Faculty of Medicine and Health TechnologyTampere UniversityTampere33720Finland
- Institute of BiotechnologyUniversity of HelsinkiHelsinki00790Finland
| | - Bengt Fadeel
- Institute of Environmental MedicineKarolinska InstitutetStockholm171 77Sweden
| |
Collapse
|
7
|
House JS, Bouzos E, Fahy KM, Francisco VM, Lloyd DT, Wright FA, Motsinger-Reif AA, Asuri P, Wheeler KE. Low-Dose Silver Nanoparticle Surface Chemistry and Temporal Effects on Gene Expression in Human Liver Cells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2000299. [PMID: 32227433 PMCID: PMC7446734 DOI: 10.1002/smll.202000299] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/29/2020] [Accepted: 03/02/2020] [Indexed: 05/31/2023]
Abstract
Silver nanoparticles (AgNPs) are widely incorporated into consumer and biomedical products for their antimicrobial and plasmonic properties with limited risk assessment of low-dose cumulative exposure in humans. To evaluate cellular responses to low-dose AgNP exposures across time, human liver cells (HepG2) are exposed to AgNPs with three different surface charges (1.2 µg mL-1 ) and complete gene expression is monitored across a 24 h period. Time and AgNP surface chemistry mediate gene expression. In addition, since cells are fed, time has marked effects on gene expression that should be considered. Surface chemistry of AgNPs alters gene transcription in a time-dependent manner, with the most dramatic effects in cationic AgNPs. Universal to all surface coatings, AgNP-treated cells responded by inactivating proliferation and enabling cell cycle checkpoints. Further analysis of these universal features of AgNP cellular response, as well as more detailed analysis of specific AgNP treatments, time points, or specific genes, is facilitated with an accompanying application. Taken together, these results provide a foundation for understanding hepatic response to low-dose AgNPs for future risk assessment.
Collapse
Affiliation(s)
- John S House
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Evangelia Bouzos
- Department of Bioengineering, Santa Clara University, Santa Clara, CA, 95053, USA
- Department of Chemistry and Biochemistry, Santa Clara University, Santa Clara, CA, 95053, USA
| | - Kira M Fahy
- Department of Chemistry and Biochemistry, Santa Clara University, Santa Clara, CA, 95053, USA
| | | | - Dillon T Lloyd
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA
| | - Fred A Wright
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA
| | - Alison A Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Prashanth Asuri
- Department of Bioengineering, Santa Clara University, Santa Clara, CA, 95053, USA
| | - Korin E Wheeler
- Department of Chemistry and Biochemistry, Santa Clara University, Santa Clara, CA, 95053, USA
| |
Collapse
|
8
|
Transcriptomics in Toxicogenomics, Part I: Experimental Design, Technologies, Publicly Available Data, and Regulatory Aspects. NANOMATERIALS 2020; 10:nano10040750. [PMID: 32326418 PMCID: PMC7221878 DOI: 10.3390/nano10040750] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 02/07/2023]
Abstract
The starting point of successful hazard assessment is the generation of unbiased and trustworthy data. Conventional toxicity testing deals with extensive observations of phenotypic endpoints in vivo and complementing in vitro models. The increasing development of novel materials and chemical compounds dictates the need for a better understanding of the molecular changes occurring in exposed biological systems. Transcriptomics enables the exploration of organisms' responses to environmental, chemical, and physical agents by observing the molecular alterations in more detail. Toxicogenomics integrates classical toxicology with omics assays, thus allowing the characterization of the mechanism of action (MOA) of chemical compounds, novel small molecules, and engineered nanomaterials (ENMs). Lack of standardization in data generation and analysis currently hampers the full exploitation of toxicogenomics-based evidence in risk assessment. To fill this gap, TGx methods need to take into account appropriate experimental design and possible pitfalls in the transcriptomic analyses as well as data generation and sharing that adhere to the FAIR (Findable, Accessible, Interoperable, and Reusable) principles. In this review, we summarize the recent advancements in the design and analysis of DNA microarray, RNA sequencing (RNA-Seq), and single-cell RNA-Seq (scRNA-Seq) data. We provide guidelines on exposure time, dose and complex endpoint selection, sample quality considerations and sample randomization. Furthermore, we summarize publicly available data resources and highlight applications of TGx data to understand and predict chemical toxicity potential. Additionally, we discuss the efforts to implement TGx into regulatory decision making to promote alternative methods for risk assessment and to support the 3R (reduction, refinement, and replacement) concept. This review is the first part of a three-article series on Transcriptomics in Toxicogenomics. These initial considerations on Experimental Design, Technologies, Publicly Available Data, Regulatory Aspects, are the starting point for further rigorous and reliable data preprocessing and modeling, described in the second and third part of the review series.
Collapse
|
9
|
Principles and applications of nanomaterial-based hyperthermia in cancer therapy. Arch Pharm Res 2020; 43:46-57. [PMID: 31993968 DOI: 10.1007/s12272-020-01206-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/09/2020] [Indexed: 12/19/2022]
Abstract
Over the past few decades, hyperthermia therapy (HTT) has become one of the most promising strategies to treat cancer. HTT has been applied with nanotechnology to overcome drawbacks such as non-selectivity and invasiveness and to maximize therapeutic efficacy. The high temperature of HTT induces protein denaturation that leads to apoptosis or necrosis. It can also enhance the effects of other cancer therapies because heat-damaged tissues reduce radioresistance and help accumulate anticancer drugs. Gold nanoparticles and superparamagnetic iron oxide with different energy sources are commonly used as hyperthermia agents. New types of nanoparticles such as those whose surface is coated with several polymers and those modified with targeting moieties have been studied as novel HTT agents. In this review, we introduce principles and applications of nanotechnology-based HTT using gold nanoparticles and superparamagnetic iron oxide.
Collapse
|
10
|
Murphy CJ, Chang HH, Falagan-Lotsch P, Gole MT, Hofmann DM, Hoang KNL, McClain SM, Meyer SM, Turner JG, Unnikrishnan M, Wu M, Zhang X, Zhang Y. Virus-Sized Gold Nanorods: Plasmonic Particles for Biology. Acc Chem Res 2019; 52:2124-2135. [PMID: 31373796 PMCID: PMC6702043 DOI: 10.1021/acs.accounts.9b00288] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Plasmons, collective oscillations of conduction-band electrons in nanoscale metals, are well-known phenomena in colloidal gold and silver nanocrystals that produce brilliant visible colors in these materials that depend on the nanocrystal size and shape. Under illumination at or near the plasmon bands, gold and silver nanocrystals exhibit properties that enable fascinating biological applications: (i) the nanocrystals elastically scatter light, providing a straightforward way to image them in complex aqueous environments; (ii) the nanocrystals produce local electric fields that enable various surface-enhanced spectroscopies for sensing, molecular diagnostics, and boosting of bound fluorophore performance; (iii) the nanocrystals produce heat, which can lead to chemical transformations at or near the nanocrystal surface and can photothermally destroy nearby cells. While all the above-mentioned applications have already been well-demonstrated in the literature, this Account focuses on several other aspects of these nanomaterials, in particular gold nanorods that are approximately the size of viruses (diameters of ∼10 nm, lengths up to 100 nm). Absolute extinction, scattering, and absorption properties are compared for gold nanorods of various absolute dimensions, and references for how to synthesize gold nanorods with four different absolute dimensions are provided. Surface chemistry strategies for coating nanocrystals with smooth or rough shells are detailed; specific examples include mesoporous silica and metal-organic framework shells for porous (rough) coatings and polyelectrolyte layer-by-layer wrapping for "smooth" shells. For self-assembled-monolayer molecular coating ligands, the smoothest shells of all, a wide range of ligand densities have been reported from many experiments, yielding values from less than 1 to nearly 10 molecules/nm2 depending on the nanocrystal size and the nature of the ligand. Systematic studies of ligand density for one particular ligand with a bulky headgroup are highlighted, showing that the highest ligand density occurs for the smallest nanocrystals, even though these ligand headgroups are the most mobile as judged by NMR relaxation studies. Biomolecular coronas form around spherical and rod-shaped nanocrystals upon immersion into biological fluids; these proteins and lipids can be quantified, and their degree of adsorption depends on the nanocrystal surface chemistry as well as the biophysical characteristics of the adsorbing biomolecule. Photothermal adsorption and desorption of proteins on nanocrystals depend on the enthalpy of protein-nanocrystal surface interactions, leading to light-triggered alteration in protein concentrations near the nanocrystals. At the cellular scale, gold nanocrystals exert genetic changes at the mRNA level, with a variety of likely mechanisms that include alteration of local biomolecular concentration gradients, changes in mechanical properties of the extracellular matrix, and physical interruption of key cellular processes-even without plasmonic effects. Microbiomes, both organismal and environmental, are the likely first point of contact of nanomaterials with natural living systems; we see a major scientific frontier in understanding, predicting, and controlling microbe-nanocrystal interactions, which may be augmented by plasmonic effects.
Collapse
Affiliation(s)
- Catherine J. Murphy
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801
| | - Huei-Huei Chang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801
| | - Priscila Falagan-Lotsch
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801
| | - Matthew T. Gole
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801
| | - Daniel M. Hofmann
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801
| | - Khoi Nguyen L. Hoang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801
| | - Sophia M. McClain
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801
| | - Sean M. Meyer
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801
| | - Jacob G. Turner
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801
| | - Mahima Unnikrishnan
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801
| | - Meng Wu
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801
| | - Xi Zhang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801
| | - Yishu Zhang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801
| |
Collapse
|
11
|
Furxhi I, Murphy F, Poland CA, Sheehan B, Mullins M, Mantecca P. Application of Bayesian networks in determining nanoparticle-induced cellular outcomes using transcriptomics. Nanotoxicology 2019; 13:827-848. [PMID: 31140895 DOI: 10.1080/17435390.2019.1595206] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Inroads have been made in our understanding of the risks posed to human health and the environment by nanoparticles (NPs) but this area requires continuous research and monitoring. Machine learning techniques have been applied to nanotoxicology with very encouraging results. This study deals with bridging physicochemical properties of NPs, experimental exposure conditions and in vitro characteristics with biological effects of NPs on a molecular cellular level from transcriptomics studies. The bridging is done by developing and implementing Bayesian Networks (BNs) with or without data preprocessing. The BN structures are derived either automatically or methodologically and compared. Early stage nanotoxicity measurements represent a challenge, not least when attempting to predict adverse outcomes and modeling is critical to understanding the biological effects of exposure to NPs. The preprocessed data-driven BN showed improved performance over automatically structured BN and the BN with unprocessed datasets. The prestructured BN captures inter relationships between NP properties, exposure condition and in vitro characteristics and links those with cellular effects based on statistic correlation findings. Information gain analysis showed that exposure dose, NP and cell line variables were the most influential attributes in predicting the biological effects. The BN methodology proposed in this study successfully predicts a number of toxicologically relevant cellular disrupted biological processes such as cell cycle and proliferation pathways, cell adhesion and extracellular matrix responses, DNA damage and repair mechanisms etc., with a success rate >80%. The model validation from independent data shows a robust and promising methodology for incorporating transcriptomics outcomes in a hazard and, by extension, risk assessment modeling framework by predicting affected cellular functions from experimental conditions.
Collapse
Affiliation(s)
- Irini Furxhi
- a Department of Accounting and Finance , Kemmy Business School University of Limerick , Limerick , Ireland
| | - Finbarr Murphy
- a Department of Accounting and Finance , Kemmy Business School University of Limerick , Limerick , Ireland
| | - Craig A Poland
- b ELEGI/Colt Laboratory , Queen's Medical Research Institute, University of Edinburgh , Edinburgh , Scotland
| | - Barry Sheehan
- a Department of Accounting and Finance , Kemmy Business School University of Limerick , Limerick , Ireland
| | - Martin Mullins
- a Department of Accounting and Finance , Kemmy Business School University of Limerick , Limerick , Ireland
| | - Paride Mantecca
- c Department of Earth and Environmental Sciences , Particulate Matter and Health Risk (POLARIS) Research Centre University of Milano Bicocca , Milano , Italy
| |
Collapse
|
12
|
Cationic gold nanoparticles elicit mitochondrial dysfunction: a multi-omics study. Sci Rep 2019; 9:4366. [PMID: 30867451 PMCID: PMC6416392 DOI: 10.1038/s41598-019-40579-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 02/19/2019] [Indexed: 01/05/2023] Open
Abstract
Systems biology is increasingly being applied in nanosafety research for observing and predicting the biological perturbations inflicted by exposure to nanoparticles (NPs). In the present study, we used a combined transcriptomics and proteomics approach to assess the responses of human monocytic cells to Au-NPs of two different sizes with three different surface functional groups, i.e., alkyl ammonium bromide, alkyl sodium carboxylate, or poly(ethylene glycol) (PEG)-terminated Au-NPs. Cytotoxicity screening using THP-1 cells revealed a pronounced cytotoxicity for the ammonium-terminated Au-NPs, while no cell death was seen after exposure to the carboxylated or PEG-modified Au-NPs. Moreover, Au-NR3+ NPs, but not the Au-COOH NPs, were found to trigger dose-dependent lethality in vivo in the model organism, Caenorhabditis elegans. RNA sequencing combined with mass spectrometry-based proteomics predicted that the ammonium-modified Au-NPs elicited mitochondrial dysfunction. The latter results were validated by using an array of assays to monitor mitochondrial function. Au-NR3+ NPs were localized in mitochondria of THP-1 cells. Moreover, the cationic Au-NPs triggered autophagy in macrophage-like RFP-GFP-LC3 reporter cells, and cell death was aggravated upon inhibition of autophagy. Taken together, these studies have disclosed mitochondria-dependent effects of cationic Au-NPs resulting in the rapid demise of the cells.
Collapse
|
13
|
Carrow JK, Cross LM, Reese RW, Jaiswal MK, Gregory CA, Kaunas R, Singh I, Gaharwar AK. Widespread changes in transcriptome profile of human mesenchymal stem cells induced by two-dimensional nanosilicates. Proc Natl Acad Sci U S A 2018; 115:E3905-E3913. [PMID: 29643075 PMCID: PMC5924886 DOI: 10.1073/pnas.1716164115] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Two-dimensional nanomaterials, an ultrathin class of materials such as graphene, nanoclays, transition metal dichalcogenides (TMDs), and transition metal oxides (TMOs), have emerged as a new generation of materials due to their unique properties relative to macroscale counterparts. However, little is known about the transcriptome dynamics following exposure to these nanomaterials. Here, we investigate the interactions of 2D nanosilicates, a layered clay, with human mesenchymal stem cells (hMSCs) at the whole-transcriptome level by high-throughput sequencing (RNA-seq). Analysis of cell-nanosilicate interactions by monitoring changes in transcriptome profile uncovered key biophysical and biochemical cellular pathways triggered by nanosilicates. A widespread alteration of genes was observed due to nanosilicate exposure as more than 4,000 genes were differentially expressed. The change in mRNA expression levels revealed clathrin-mediated endocytosis of nanosilicates. Nanosilicate attachment to the cell membrane and subsequent cellular internalization activated stress-responsive pathways such as mitogen-activated protein kinase (MAPK), which subsequently directed hMSC differentiation toward osteogenic and chondrogenic lineages. This study provides transcriptomic insight on the role of surface-mediated cellular signaling triggered by nanomaterials and enables development of nanomaterials-based therapeutics for regenerative medicine. This approach in understanding nanomaterial-cell interactions illustrates how change in transcriptomic profile can predict downstream effects following nanomaterial treatment.
Collapse
Affiliation(s)
- James K Carrow
- Department of Biomedical Engineering, Texas A&M University, College Station, TX 77843
| | - Lauren M Cross
- Department of Biomedical Engineering, Texas A&M University, College Station, TX 77843
| | - Robert W Reese
- Department of Biomedical Engineering, Texas A&M University, College Station, TX 77843
| | - Manish K Jaiswal
- Department of Biomedical Engineering, Texas A&M University, College Station, TX 77843
| | - Carl A Gregory
- Department of Molecular and Cellular Medicine, Institute of Regenerative Medicine, Texas A&M Health Science Center, College Station, TX 77843
| | - Roland Kaunas
- Department of Biomedical Engineering, Texas A&M University, College Station, TX 77843
| | - Irtisha Singh
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065;
- Tri-I Program in Computational Biology and Medicine, Weill Cornell Graduate College, New York, NY 10065
| | - Akhilesh K Gaharwar
- Department of Biomedical Engineering, Texas A&M University, College Station, TX 77843;
- Department of Material Sciences, Texas A&M University, College Station, TX 77843
- Center for Remote Health Technologies and Systems, Texas A&M University, College Station, TX 77843
| |
Collapse
|
14
|
Dennison JM, Zupancic JM, Lin W, Dwyer JH, Murphy CJ. Protein Adsorption to Charged Gold Nanospheres as a Function of Protein Deformability. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:7751-7761. [PMID: 28704605 DOI: 10.1021/acs.langmuir.7b01909] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The corona that forms as protein adsorbs to gold nanospheres (AuNSs) is directly influenced by the surface chemistry of the AuNS. Tools to predict adsorption outcomes are needed for intelligent design of nanomaterials for biological applications. We hypothesized that the denaturation behavior of a protein might be a useful predictor of adsorption behavior to AuNSs, and used this idea to study protein adsorption to anionic citrate-capped AuNSs and to cationic poly(allylamine hydrochloride) (PAH) wrapped AuNSs. Three proteins (α-amylase (A-Amy), β-lactoglobulin (BLG), and bovine serum albumin (BSA)), representing three different classes of acid denaturation behavior, were selected with BLG being the least deformable and BSA being the most deformable. Protein adsorption to AuNSs was monitored via UV-vis spectrophotometry and dynamic light scattering. Changes to the protein structure upon AuNS interaction were monitored via circular dichroism spectroscopy. Binding constants were determined using the Langmuir adsorption isotherm, resulting in BSA > BLG ≫ A-Amy affinities for citrate-capped gold nanospheres. PAH-coated AuNSs displayed little affinity for these proteins at similar concentrations as citrate-coated AuNSs and became agglomerated at high protein concentrations. The enzymatic activity of A-Amy/citrate AuNS conjugates was measured via colorimetric assay, and found to be 11% of free A-Amy, suggesting that binding restricts access to the active site. Across both citrate AuNSs and PAH AuNSs, the changes in secondary structure were greatest for BSA > A-Amy > BLG, which does follow the trends predicted by acid denaturation characteristics.
Collapse
Affiliation(s)
- Jordan M Dennison
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 Mathews Avenue, Urbana, Illinois 61801, United States
| | - Jennifer M Zupancic
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 Mathews Avenue, Urbana, Illinois 61801, United States
| | - Wayne Lin
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 Mathews Avenue, Urbana, Illinois 61801, United States
| | - Jonathan H Dwyer
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 Mathews Avenue, Urbana, Illinois 61801, United States
| | - Catherine J Murphy
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 Mathews Avenue, Urbana, Illinois 61801, United States
| |
Collapse
|
15
|
Falagan-Lotsch P, Grzincic EM, Murphy CJ. New Advances in Nanotechnology-Based Diagnosis and Therapeutics for Breast Cancer: An Assessment of Active-Targeting Inorganic Nanoplatforms. Bioconjug Chem 2017; 28:135-152. [DOI: 10.1021/acs.bioconjchem.6b00591] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Priscila Falagan-Lotsch
- Department
of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Elissa M. Grzincic
- Department
of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Catherine J. Murphy
- Department
of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| |
Collapse
|
16
|
One low-dose exposure of gold nanoparticles induces long-term changes in human cells. Proc Natl Acad Sci U S A 2016; 113:13318-13323. [PMID: 27821760 DOI: 10.1073/pnas.1616400113] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We report the in vitro long-term (20 wk) changes in cells exposed to well-characterized gold nanoparticles (Au NPs) with varying shapes and surface coatings under both chronic (exposure to Au NPs continuously over 20 wk) and nonchronic (initial acute cell exposure to Au NPs, followed by 20 wk in NP-free cell media) conditions. Both chronic and nonchronic Au NPs exposures at low dose induce modifications at the gene level after long periods. In attempt to overcome from the injuries caused by nanoparticle exposure, genes related to oxidative stress, cell cycle regulation, and inflammation are among those presenting differential expression levels. Surprisingly, the nonchronic exposure induced more gene expression changes than its chronic counterpart and the stress effects caused by this type of exposure were sustained even after 20 wk without any additional NP exposure. NP surface chemistry played an important role in the alteration of gene regulation. Overall, our data suggest that (i) cells can adaptively respond to chronic, low-level NP insults; (ii) the cell stress response is not reversible over time upon removal of NPs upon acute, nonchronic exposure; and (iii) polyethylene glycol is not as benign a surface chemistry as is generally supposed.
Collapse
|
17
|
Burrows ND, Lin W, Hinman JG, Dennison JM, Vartanian AM, Abadeer NS, Grzincic EM, Jacob LM, Li J, Murphy CJ. Surface Chemistry of Gold Nanorods. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:9905-9921. [PMID: 27568788 DOI: 10.1021/acs.langmuir.6b02706] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Gold nanorods have garnered a great deal of scientific interest because of their unique optical properties, and they have the potential to greatly impact many areas of science and technology. Understanding the structure and chemical makeup of their surfaces as well as how to tailor them is of paramount importance in the development of their successful applications. This Feature Article reviews the current understanding of the surface chemistry of as-synthesized gold nanorods, methods of tailoring the surface chemistry of gold nanorods with various inorganic and organic coatings/ligands, and the techniques employed to characterize ligands on the surface of gold nanorods as well as the associated measurement challenges. Specifically, we address the challenges of determining how thick the ligand shell is, how many ligands per nanorod are present on the surface, and where the ligands are located in regiospecific and mixed-ligand systems. We conclude with an outlook on the development of the surface chemistry of gold nanorods leading to the development of a synthetic nanoparticle surface chemistry toolbox analogous to that of synthetic organic chemistry and natural product synthesis.
Collapse
Affiliation(s)
- Nathan D Burrows
- Department of Chemistry, 600 S. Mathews Avenue, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Wayne Lin
- Department of Chemistry, 600 S. Mathews Avenue, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Joshua G Hinman
- Department of Chemistry, 600 S. Mathews Avenue, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Jordan M Dennison
- Department of Chemistry, 600 S. Mathews Avenue, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Ariane M Vartanian
- Department of Chemistry, 600 S. Mathews Avenue, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Nardine S Abadeer
- Department of Chemistry, 600 S. Mathews Avenue, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Elissa M Grzincic
- Department of Chemistry, 600 S. Mathews Avenue, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Lisa M Jacob
- Department of Chemistry, 600 S. Mathews Avenue, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Ji Li
- Department of Chemistry, 600 S. Mathews Avenue, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Catherine J Murphy
- Department of Chemistry, 600 S. Mathews Avenue, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| |
Collapse
|
18
|
Hinman JG, Stork AJ, Varnell JA, Gewirth AA, Murphy CJ. Seed mediated growth of gold nanorods: towards nanorod matryoshkas. Faraday Discuss 2016; 191:9-33. [PMID: 27442269 DOI: 10.1039/c6fd00145a] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
After a brief review of anisotropy on the nanoscale, experiments in which nanorod core-shell-shell particles are grown are presented. These "nanomatryoshkas" consist of a gold nanorod core, a silica shell, and a final gold shell. Calculation of the near-field properties of these structures using the discrete dipole approximation uncovers the change in location of local electric fields upon gold outer shell growth. Electrochemical experiments of the weak reducing agents used to grow the gold nanorod cores suggest a correlation between the strength of the reducing agent and its ability to promote longer nanorod growth. The final nanostructures do not exhibit a smooth outer shell, unlike their spherical counterparts.
Collapse
Affiliation(s)
- Joshua G Hinman
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, Il 61801, USA.
| | | | | | | | | |
Collapse
|
19
|
Oh JH, Son MY, Choi MS, Kim S, Choi AY, Lee HA, Kim KS, Kim J, Song CW, Yoon S. Integrative analysis of genes and miRNA alterations in human embryonic stem cells-derived neural cells after exposure to silver nanoparticles. Toxicol Appl Pharmacol 2015; 299:8-23. [PMID: 26551752 DOI: 10.1016/j.taap.2015.11.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 10/31/2015] [Accepted: 11/05/2015] [Indexed: 12/31/2022]
Abstract
Given the rapid growth of engineered and customer products made of silver nanoparticles (Ag NPs), understanding their biological and toxicological effects on humans is critically important. The molecular developmental neurotoxic effects associated with exposure to Ag NPs were analyzed at the physiological and molecular levels, using an alternative cell model: human embryonic stem cell (hESC)-derived neural stem/progenitor cells (NPCs). In this study, the cytotoxic effects of Ag NPs (10-200μg/ml) were examined in these hESC-derived NPCs, which have a capacity for neurogenesis in vitro, at 6 and 24h. The results showed that Ag NPs evoked significant toxicity in hESC-derived NPCs at 24h in a dose-dependent manner. In addition, Ag NPs induced cell cycle arrest and apoptosis following a significant increase in oxidative stress in these cells. To further clarify the molecular mechanisms of the toxicological effects of Ag NPs at the transcriptional and post-transcriptional levels, the global expression profiles of genes and miRNAs were analyzed in hESC-derived NPCs after Ag NP exposure. The results showed that Ag NPs induced oxidative stress and dysfunctional neurogenesis at the molecular level in hESC-derived NPCs. Based on this hESC-derived neural cell model, these findings have increased our understanding of the molecular events underlying developmental neurotoxicity induced by Ag NPs in humans.
Collapse
Affiliation(s)
- Jung-Hwa Oh
- Korea Institute of Toxicology (KIT), Daejeon 34114, Republic of Korea; Department of human and environmental toxicology, University of Science & Technology, Daejeon 34113, Republic of Korea
| | - Mi-Young Son
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahangno, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of functional genomics, University of Science & Technology, 217 Gajungro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Mi-Sun Choi
- Korea Institute of Toxicology (KIT), Daejeon 34114, Republic of Korea
| | - Soojin Kim
- Korea Institute of Toxicology (KIT), Daejeon 34114, Republic of Korea
| | - A-Young Choi
- Korea Institute of Toxicology (KIT), Daejeon 34114, Republic of Korea
| | - Hyang-Ae Lee
- Korea Institute of Toxicology (KIT), Daejeon 34114, Republic of Korea; Department of human and environmental toxicology, University of Science & Technology, Daejeon 34113, Republic of Korea
| | - Ki-Suk Kim
- Korea Institute of Toxicology (KIT), Daejeon 34114, Republic of Korea; Department of human and environmental toxicology, University of Science & Technology, Daejeon 34113, Republic of Korea
| | - Janghwan Kim
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahangno, Yuseong-gu, Daejeon 34141, Republic of Korea; Department of functional genomics, University of Science & Technology, 217 Gajungro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Chang Woo Song
- Korea Institute of Toxicology (KIT), Daejeon 34114, Republic of Korea; Department of human and environmental toxicology, University of Science & Technology, Daejeon 34113, Republic of Korea.
| | - Seokjoo Yoon
- Korea Institute of Toxicology (KIT), Daejeon 34114, Republic of Korea; Department of human and environmental toxicology, University of Science & Technology, Daejeon 34113, Republic of Korea.
| |
Collapse
|
20
|
Yi G, Yuan J, Bi H, Yan W, Yang N, Qu L. In-Depth Duodenal Transcriptome Survey in Chickens with Divergent Feed Efficiency Using RNA-Seq. PLoS One 2015; 10:e0136765. [PMID: 26418546 PMCID: PMC4721924 DOI: 10.1371/journal.pone.0136765] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 08/07/2015] [Indexed: 12/19/2022] Open
Abstract
Since the feed cost is a major determinant of profitability in poultry industry, how to improve feed efficiency through genetic selection is an intriguing subject for breeders and producers. As a more suitable indicator assessing feed efficiency, residual feed intake (RFI) is defined as the difference between observed and expected feed intake based on maintenance and growth. However, the genetic mechanisms responsible for RFI in chickens are still less well appreciated. In this study, we investigated the duodenal transcriptome architecture of extreme RFI phenotypes in the six brown-egg dwarf hens (three per group) using RNA sequencing technology. Among all mapped reads, an average of 75.62% fell into annotated exons, 5.50% were located in introns, and the remaining 18.88% were assigned to intergenic regions. In total, we identified 41 promising candidate genes by differential expression analysis between the low and high RFI groups. Furthermore, qRT-PCR assays were designed for 10 randomly chosen genes, and nine (90.00%) were successfully validated. Functional annotation analyses revealed that these significant genes belong to several specific biological functions related to digestibility, metabolism and biosynthesis processes as well as energy homeostasis. We also predicted 253 intergenic coding transcripts, and these transcripts were mainly involved in fundamental biological regulation and metabolism processes. Our findings provided a pioneering exploration of biological basis underlying divergent RFI using RNA-Seq, which pinpoints promising candidate genes of functional relevance, is helpful to guide future breeding strategies to optimize feed efficiency and assists in improving the current gene annotation in chickens.
Collapse
Affiliation(s)
- Guoqiang Yi
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jingwei Yuan
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Huijuan Bi
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Wei Yan
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lujiang Qu
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- * E-mail:
| |
Collapse
|
21
|
Grzincic EM, Murphy CJ. Gold Nanorods Indirectly Promote Migration of Metastatic Human Breast Cancer Cells in Three-Dimensional Cultures. ACS NANO 2015; 9:6801-6816. [PMID: 26118624 DOI: 10.1021/acsnano.5b03362] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Gold nanomaterials are intensively studied for applications in disease detection, diagnosis and therapeutics, and this has motivated considerable research to determine their interaction with biomolecules, cells and cell behaviors. However, few studies look at how nanomaterials alter the extracellular matrix (ECM) and cell-ECM interactions. Nanomaterials in the body would interact with the entire cellular environment, and it is imperative to account for this when studying the impact of nanomaterials on living systems. Furthermore, recent evidence finds that migration rates of cells in 2D can be affected by nanomaterials, and uptake of the nanomaterials is not necessary to exert an effect. In this study, three-dimensional nested type I collagen matrices were utilized as a model ECM to study how gold nanorods affect the migration of MDA-MB-231 human breast cancer cells. Spontaneous cell migration through collagen containing gold nanorods was found to increase with increasing concentrations of gold nanorods, independent of intracellular uptake of the nanorods. Gold nanorods in the collagen matrix were found to alter collagen mechanical properties and structure, molecular diffusion, cellular adhesion, cell morphology, mode of migration and protease expression. Correlation between decreased cellular adhesion and rounded cell morphology and locomotion in nanorod-containing collagen suggests the induction of an amoeboid-like migratory phenotype.
Collapse
Affiliation(s)
- Elissa M Grzincic
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Catherine J Murphy
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| |
Collapse
|
22
|
Murphy CJ, Vartanian A. Biological Responses to Engineered Nanomaterials: Needs for the Next Decade. ACS CENTRAL SCIENCE 2015; 1:117-23. [PMID: 27162961 PMCID: PMC4827556 DOI: 10.1021/acscentsci.5b00182] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Indexed: 05/20/2023]
Abstract
The interaction of nanomaterials with biomolecules, cells, and organisms is an enormously vital area of current research, with applications in nanoenabled diagnostics, imaging agents, therapeutics, and contaminant removal technologies. Yet the potential for adverse biological and environmental impacts of nanomaterial exposure is considerable and needs to be addressed to ensure sustainable development of nanomaterials. In this Outlook four research needs for the next decade are outlined: (i) measurement of the chemical nature of nanomaterials in dynamic, complex aqueous environments; (ii) real-time measurements of nanomaterial-biological interactions with chemical specificity; (iii) delineation of molecular modes of action for nanomaterial effects on living systems as functions of nanomaterial properties; and (iv) an integrated systems approach that includes computation and simulation across orders of magnitude in time and space.
Collapse
Affiliation(s)
- Catherine J. Murphy
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Ariane
M. Vartanian
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| |
Collapse
|