1
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Deleye L, Franchi F, Trevisani M, Loiacono F, Vercellino S, Debellis D, Liessi N, Armirotti A, Vázquez E, Valente P, Castagnola V, Benfenati F. Few-layered graphene increases the response of nociceptive neurons to irritant stimuli. Nanoscale 2024; 16:2419-2431. [PMID: 38226500 DOI: 10.1039/d3nr03790h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
The unique properties of few-layered graphene (FLG) make it interesting for a variety of applications, including biomedical applications, such as tissue engineering and drug delivery. Although different studies focus on applications in the central nervous system, its interaction with the peripheral nervous system has been so far overlooked. Here, we investigated the effects of exposure to colloidal dispersions of FLG on the sensory neurons of the rat dorsal root ganglia (DRG). We found that the FLG flakes were actively internalized by sensory neurons, accumulated in large intracellular vesicles, and possibly degraded over time, without major toxicological concerns, as neuronal viability, morphology, protein content, and basic electrical properties of DRG neurons were preserved. Interestingly, in our electrophysiological investigation under noxious stimuli, we observed an increased functional response upon FLG treatment of the nociceptive subpopulation of DRG neurons in response to irritants specific for chemoreceptors TRPV1 and TRPA1. The observed effects of FLG on DRG neurons may open-up novel opportunities for applications of these materials in specific disease models.
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Affiliation(s)
- Lieselot Deleye
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia (IIT), Largo Rosanna Benzi 10, 16132 Genova, Italy.
| | - Francesca Franchi
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia (IIT), Largo Rosanna Benzi 10, 16132 Genova, Italy.
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genova, Italy
| | - Martina Trevisani
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia (IIT), Largo Rosanna Benzi 10, 16132 Genova, Italy.
- Department of Experimental Medicine, Section of Physiology, University of Genova, Genoa, 16132, Italy.
| | - Fabrizio Loiacono
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genova, Italy
| | - Silvia Vercellino
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia (IIT), Largo Rosanna Benzi 10, 16132 Genova, Italy.
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genova, Italy
| | - Doriana Debellis
- Electron Microscopy Facility, IIT, Via Morego 30, 16163, Genoa, Italy
| | - Nara Liessi
- Analytical Chemistry Facility, IIT, via Morego, 30, 16163, Genoa, Italy
| | - Andrea Armirotti
- Analytical Chemistry Facility, IIT, via Morego, 30, 16163, Genoa, Italy
| | - Ester Vázquez
- Facultad de Ciencias Químicas, Universidad Castilla La-Mancha, Ciudad Real, 13071 Spain
| | - Pierluigi Valente
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genova, Italy
- Department of Experimental Medicine, Section of Physiology, University of Genova, Genoa, 16132, Italy.
| | - Valentina Castagnola
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia (IIT), Largo Rosanna Benzi 10, 16132 Genova, Italy.
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genova, Italy
| | - Fabio Benfenati
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia (IIT), Largo Rosanna Benzi 10, 16132 Genova, Italy.
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genova, Italy
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2
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Castagnola V, Deleye L, Podestà A, Jaho E, Loiacono F, Debellis D, Trevisani M, Ciobanu DZ, Armirotti A, Pisani F, Flahaut E, Vazquez E, Bramini M, Cesca F, Benfenati F. Interactions of Graphene Oxide and Few-Layer Graphene with the Blood-Brain Barrier. Nano Lett 2023; 23:2981-2990. [PMID: 36917703 PMCID: PMC10103300 DOI: 10.1021/acs.nanolett.3c00377] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/03/2023] [Indexed: 06/18/2023]
Abstract
Thanks to their biocompatibility and high cargo capability, graphene-based materials (GRMs) might represent an ideal brain delivery system. The capability of GRMs to reach the brain has mainly been investigated in vivo and has highlighted some controversy. Herein, we employed two in vitro BBB models of increasing complexity to investigate the bionano interactions with graphene oxide (GO) and few-layer graphene (FLG): a 2D murine Transwell model, followed by a 3D human multicellular assembloid, to mimic the complexity of the in vivo architecture and intercellular crosstalk. We developed specific methodologies to assess the translocation of GO and FLG in a label-free fashion and a platform applicable to any nanomaterial. Overall, our results show good biocompatibility of the two GRMs, which did not impact the integrity and functionality of the barrier. Sufficiently dispersed subpopulations of GO and FLG were actively uptaken by endothelial cells; however, the translocation was identified as a rare event.
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Affiliation(s)
- Valentina Castagnola
- Center
for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Largo Rosanna Benzi 10, 16132 Genova, Italy
- IRCCS
Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genova, Italy
| | - Lieselot Deleye
- Center
for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Largo Rosanna Benzi 10, 16132 Genova, Italy
| | - Alice Podestà
- Center
for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Largo Rosanna Benzi 10, 16132 Genova, Italy
| | - Edra Jaho
- Center
for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Largo Rosanna Benzi 10, 16132 Genova, Italy
| | - Fabrizio Loiacono
- IRCCS
Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genova, Italy
| | - Doriana Debellis
- Electron
Microscopy Facility, Istituto Italiano di
Tecnologia, Via Morego, 30, 16163 Genova, Italy
| | - Martina Trevisani
- Center
for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Largo Rosanna Benzi 10, 16132 Genova, Italy
- Department
of Experimental Medicine, Università
degli Studi di Genova, 16132 Genova, Italy
| | - Dinu Zinovie Ciobanu
- Analytical
Chemistry Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Andrea Armirotti
- Analytical
Chemistry Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Francesco Pisani
- Center
for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Largo Rosanna Benzi 10, 16132 Genova, Italy
- Department
of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari “Aldo Moro”, Bari 70121, Italy
| | - Emmanuel Flahaut
- CIRIMAT,
UMR 5085, CNRS-INP-UPS, Université
Toulouse 3 Paul Sabatier, 118 route de Narbonne, F-31062 Toulouse cedex 9, France
| | - Ester Vazquez
- Instituto
Regional de Investigación Científica Aplicada (IRICA), Universidad de Castilla-La Mancha, 13071 Ciudad Real, Spain
- Facultad
de Ciencias y Tecnologías Químicas, Universidad de Castilla-La Mancha, Avda. Camilo José Cela S/N, 13071 Ciudad Real, Spain
| | - Mattia Bramini
- Center
for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Largo Rosanna Benzi 10, 16132 Genova, Italy
- Department
of Cell Biology, Universidad de Granada, C. Fuentenueva s/n, 18071 Granada, Spain
| | - Fabrizia Cesca
- Center
for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Largo Rosanna Benzi 10, 16132 Genova, Italy
- Department
of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Fabio Benfenati
- Center
for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Largo Rosanna Benzi 10, 16132 Genova, Italy
- IRCCS
Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genova, Italy
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3
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Iachetta G, Colistra N, Melle G, Deleye L, Tantussi F, De Angelis F, Dipalo M. Improving reliability and reducing costs of cardiotoxicity assessments using laser-induced cell poration on microelectrode arrays. Toxicol Appl Pharmacol 2021; 418:115480. [PMID: 33689843 DOI: 10.1016/j.taap.2021.115480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/07/2021] [Accepted: 03/02/2021] [Indexed: 10/22/2022]
Abstract
Drug-induced cardiotoxicity is a major barrier to drug development and a main cause of withdrawal of marketed drugs. Drugs can strongly alter the spontaneous functioning of the heart by interacting with the cardiac membrane ion channels. If these effects only surface during in vivo preclinical tests, clinical trials or worse after commercialization, the societal and economic burden will be significant and seriously hinder the efficient drug development process. Hence, cardiac safety pharmacology requires in vitro electrophysiological screening assays of all drug candidates to predict cardiotoxic effects before clinical trials. In the past 10 years, microelectrode array (MEA) technology began to be considered a valuable approach in pharmaceutical applications. However, an effective tool for high-throughput intracellular measurements, compatible with pharmaceutical standards, is not yet available. Here, we propose laser-induced optoacoustic poration combined with CMOS-MEA technology as a reliable and effective platform to detect cardiotoxicity. This approach enables the acquisition of high-quality action potential recordings from large numbers of cardiomyocytes within the same culture well, providing reliable data using single-well MEA devices and single cardiac syncytia per each drug. Thus, this technology could be applied in drug safety screening platforms reducing times and costs of cardiotoxicity assessments, while simultaneously improving the data reliability.
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Affiliation(s)
| | - Nicolò Colistra
- Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Giovanni Melle
- Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Lieselot Deleye
- Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | | | | | - Michele Dipalo
- Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy.
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4
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Barbaglia A, Dipalo M, Melle G, Iachetta G, Deleye L, Hubarevich A, Toma A, Tantussi F, De Angelis F. Mirroring Action Potentials: Label-Free, Accurate, and Noninvasive Electrophysiological Recordings of Human-Derived Cardiomyocytes. Adv Mater 2021; 33:e2004234. [PMID: 33410191 DOI: 10.1002/adma.202004234] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 11/15/2020] [Indexed: 05/23/2023]
Abstract
The electrophysiological recording of action potentials in human cells is a long-sought objective due to its pivotal importance in many disciplines. Among the developed techniques, invasiveness remains a common issue, causing cytotoxicity or altering unpredictably cell physiological response. In this work, a new approach for recording intracellular signals of outstanding quality and with noninvasiveness is introduced. By taking profit of the concept of mirror charge in classical electrodynamics, the new proposed device transduces cell ionic currents into mirror charges in a microfluidic chamber, thus realizing a virtual mirror cell. By monitoring mirror charge dynamics, it is possible to effectively record the action potentials fired by the cells. Since there is no need for accessing or interacting with the cells, the method is intrinsically noninvasive. In addition, being based on optical recording, it shows high spatial resolution and high parallelization. As shown through a set of experiments, the presented methodology is an ideal candidate for the next generation devices for the reliable assessment of cardiotoxicity on human-derived cardiomyocytes. More generally, it paves the way toward a new family of in vitro biodevices that will lay a new milestone in the field of electrophysiology.
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Affiliation(s)
- Andrea Barbaglia
- Istituto Italiano di Tecnologia, Via Morego 30, Genova, 16163, Italy
| | - Michele Dipalo
- Istituto Italiano di Tecnologia, Via Morego 30, Genova, 16163, Italy
| | - Giovanni Melle
- Istituto Italiano di Tecnologia, Via Morego 30, Genova, 16163, Italy
| | | | - Lieselot Deleye
- Istituto Italiano di Tecnologia, Via Morego 30, Genova, 16163, Italy
| | | | - Andrea Toma
- Istituto Italiano di Tecnologia, Via Morego 30, Genova, 16163, Italy
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5
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d'Amora M, Colucci P, Usai A, Landi E, Deleye L, Dente L, De Angelis F, Raffa V, Tantussi F. Heat-sensitive poly-acrylamide nanoparticle for cancer treatment. Precision Nanomedicine 2020. [DOI: 10.33218/001c.17629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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6
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Bruno G, Colistra N, Melle G, Cerea A, Hubarevich A, Deleye L, De Angelis F, Dipalo M. Microfluidic Multielectrode Arrays for Spatially Localized Drug Delivery and Electrical Recordings of Primary Neuronal Cultures. Front Bioeng Biotechnol 2020; 8:626. [PMID: 32656200 PMCID: PMC7325920 DOI: 10.3389/fbioe.2020.00626] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/21/2020] [Indexed: 12/15/2022] Open
Abstract
Neuropathological models and neurological disease progression and treatments have always been of great interest in biomedical research because of their impact on society. The application of in vitro microfluidic devices to neuroscience-related disciplines provided several advancements in therapeutics or neuronal modeling thanks to the ability to control the cellular microenvironment at spatiotemporal level. Recently, the introduction of three-dimensional nanostructures has allowed high performance in both in vitro recording of electrogenic cells and drug delivery using minimally invasive devices. Independently, both delivery and recording have let to pioneering solutions in neurobiology. However, their combination on a single chip would provide further fundamental improvements in drug screening systems and would offer comprehensive insights into pathologies and diseases progression. Therefore, it is crucial to develop platforms able to monitor progressive changes in electrophysiological behavior in the electrogenic cellular network, induced by spatially localized injection of biochemical agents. In this work, we show the application of a microfluidic multielectrode array (MEA) platform to record spontaneous and chemically stimulated activity in primary neuronal networks. By means of spatially localized caffeine injection via microfluidic nanochannels, the device demonstrated its capability of combined localized drug delivery and cell signaling recording. The platform could detect activity of the neural network at multiple sites while delivering molecules into just a few selected cells, thereby examining the effect of biochemical agents on the desired portion of cell culture.
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Affiliation(s)
- Giulia Bruno
- DIBRIS, Università degli Studi di Genova, Genoa, Italy.,Istituto Italiano di Tecnologia, Genoa, Italy
| | | | - Giovanni Melle
- DIBRIS, Università degli Studi di Genova, Genoa, Italy.,Istituto Italiano di Tecnologia, Genoa, Italy
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7
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Huang JA, Caprettini V, Zhao Y, Melle G, Maccaferri N, Deleye L, Zambrana-Puyalto X, Ardini M, Tantussi F, Dipalo M, De Angelis F. On-Demand Intracellular Delivery of Single Particles in Single Cells by 3D Hollow Nanoelectrodes. Nano Lett 2019; 19:722-731. [PMID: 30673248 PMCID: PMC6378653 DOI: 10.1021/acs.nanolett.8b03764] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Delivery of molecules into intracellular compartments is one of the fundamental requirements in molecular biology. However, the possibility of delivering a precise number of nano-objects with single-particle resolution is still an open challenge. Here we present an electrophoretic platform based on 3D hollow nanoelectrodes to enable delivery of single nanoparticles into single selected cells and monitoring of the single-particle delivery by surface-enhanced Raman scattering (SERS). The gold-coated hollow nanoelectrode capable of confinement and enhancement of electromagnetic fields upon laser illumination can distinguish the SERS signals of a single nanoparticle flowing through the nanoelectrode. Tight wrapping of cell membranes around the nanoelectrodes allows effective membrane electroporation such that single gold nanorods are delivered on demand into a living cell by electrophoresis. The capability of the 3D hollow nanoelectrodes to porate cells and reveal single emitters from the background in continuous flow is promising for the analysis of both intracellular delivery and sampling.
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Affiliation(s)
- Jian-An Huang
- Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Valeria Caprettini
- Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
- DIBRIS, University of Genoa, Via all’Opera Pia 13, 16145 Genova, Italy
| | - Yingqi Zhao
- Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Giovanni Melle
- Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
- DIBRIS, University of Genoa, Via all’Opera Pia 13, 16145 Genova, Italy
| | | | - Lieselot Deleye
- Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | | | - Matteo Ardini
- Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | | | - Michele Dipalo
- Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
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8
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Deleye L, Gansemans Y, De Coninck D, Van Nieuwerburgh F, Deforce D. Massively parallel sequencing of micro-manipulated cells targeting a comprehensive panel of disease-causing genes: A comparative evaluation of upstream whole-genome amplification methods. PLoS One 2018; 13:e0196334. [PMID: 29698522 PMCID: PMC5919401 DOI: 10.1371/journal.pone.0196334] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 04/11/2018] [Indexed: 12/28/2022] Open
Abstract
Single Gene Disorders (SGD) are still routinely diagnosed using PCR-based assays that need to be developed and validated for each individual disease-specific gene fragment. The TruSight One sequencing panel currently covers 12 Mb of genomic content, including 4813 genes associated with a clinical phenotype. When only a limited number of cells are available, whole genome amplification (WGA) is required prior to DNA target capture techniques such as the TruSight One panel. In this study, we compared 4 different WGA methods in combination with the TruSight One sequencing panel to perform single nucleotide polymorphism (SNP) genotyping starting from 3 micro-manipulated cells. This setting simulates clinical settings such as day-5 blastocyst biopsy for Preimplantation Genetic Testing (PGT), liquid biopsy of circulating tumor cells (CTCs) and cancer-cell profiling. Bulk cell samples were processed alongside these WGA samples to serve as a performance reference. Target coverage, coverage uniformity and SNP calling accuracy obtained using any of the WGA, is inferior to the results obtained on bulk cell samples. However, results after REPLI-g come close. Compared to the other WGA methods, the method using REPLI-g WGA results in a better coverage of the targeted genomic regions with a more uniform read depth. Consequently, this method also results in a more accurate SNP calling and could be considered for clinical genotyping of a limited number of cells.
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Affiliation(s)
- Lieselot Deleye
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Yannick Gansemans
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Dieter De Coninck
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | | | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
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9
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Deleye L, Vander Plaetsen AS, Weymaere J, Deforce D, Van Nieuwerburgh F. Short Tandem Repeat analysis after Whole Genome Amplification of single B-lymphoblastoid cells. Sci Rep 2018; 8:1255. [PMID: 29352241 PMCID: PMC5775416 DOI: 10.1038/s41598-018-19509-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 01/02/2018] [Indexed: 11/30/2022] Open
Abstract
To allow multiple genetic analyses on a single cell, whole genome amplification (WGA) is required. Unfortunately, studies comparing different WGA methods for downstream human identification Short Tandem Repeat (STR) analysis remain absent. Therefore, the aim of this work was to assess the performance of four commercially available WGA kits for downstream human identification STR profiling on a B-lymphoblastoid cell line. The performance was assessed using an input of one or three micromanipulated cells. REPLI-g showed a very low dropout rate, as it was the only WGA method in this study that could provide a complete STR profile in some of its samples. Although Ampli1, DOPlify and PicoPLEX did not detect all selected STR markers, they seem suitable for genetic identification in single-cell applications.
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Affiliation(s)
- Lieselot Deleye
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Ann-Sophie Vander Plaetsen
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Jana Weymaere
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium.
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10
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Abstract
Shallow whole genome sequencing has recently been introduced for genome-wide detection of chromosomal copy number alterations (CNAs) in preimplantation genetic diagnosis (PGD), using only 4-7 trophectoderm cells biopsied from day-5 embryos. This chapter describes the complete method, starting from whole genome amplification (WGA) on isolated blastomere(s), up to data analysis for CNA detection. The process is described generically and can also be used to perform CNA analysis on a limited number of cells (down to a single cell) in other applications. This unique description also includes some tips and tricks to increase the chance of success.
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Affiliation(s)
- Lieselot Deleye
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Dieter De Coninck
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium.
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11
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Vander Plaetsen AS, Deleye L, Cornelis S, Tilleman L, Van Nieuwerburgh F, Deforce D. STR profiling and Copy Number Variation analysis on single, preserved cells using current Whole Genome Amplification methods. Sci Rep 2017; 7:17189. [PMID: 29215049 PMCID: PMC5719346 DOI: 10.1038/s41598-017-17525-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/15/2017] [Indexed: 01/01/2023] Open
Abstract
The growing interest in liquid biopsies for cancer research and cell-based non-invasive prenatal testing (NIPT) invigorates the need for improved single cell analysis. In these applications, target cells are extremely rare and fragile in peripheral circulation, which makes the genetic analysis very challenging. To overcome these challenges, cell stabilization and unbiased whole genome amplification are required. This study investigates the performance of four WGA methods on single or a limited number of cells after 24 hour of Streck Cell-Free DNA BCT preservation. The suitability of the DNA, amplified with Ampli1, DOPlify, PicoPLEX and REPLI-g, was assessed for both short tandem repeat (STR) profiling and copy number variant (CNV) analysis after shallow whole genome massively parallel sequencing (MPS). Results demonstrate that Ampli1, DOPlify and PicoPLEX perform well for both applications, with some differences between the methods. Samples amplified with REPLI-g did not result in suitable STR or CNV profiles, indicating that this WGA method is not able to generate high quality DNA after Streck Cell-Free DNA BCT stabilization of the cells.
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Affiliation(s)
- Ann-Sophie Vander Plaetsen
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Lieselot Deleye
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Senne Cornelis
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium.,Department of Life Science Technologies, imec, 3001, Leuven, Belgium
| | - Laurentijn Tilleman
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium.
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
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12
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Deleye L, Tilleman L, Vander Plaetsen AS, Cornelis S, Deforce D, Van Nieuwerburgh F. Performance of four modern whole genome amplification methods for copy number variant detection in single cells. Sci Rep 2017; 7:3422. [PMID: 28611458 PMCID: PMC5469777 DOI: 10.1038/s41598-017-03711-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 05/05/2017] [Indexed: 12/22/2022] Open
Abstract
Whole genome amplification (WGA) has become an invaluable tool to perform copy number variation (CNV) detection in single, or a limited number of cells. Unfortunately, current WGA methods introduce representation bias that limits the detection of small CNVs. New WGA methods have been introduced that might have the potential to reduce this bias. We compared the performance of PicoPLEX DNA-Seq (Picoseq), DOPlify, REPLI-g and Ampli-1 WGA for aneuploidy screening and copy number analysis using shallow whole genome massively parallel sequencing (MPS), starting from single or a limited number of cells. Although the four WGA methods perform differently, they are all suited for this application.
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Affiliation(s)
- Lieselot Deleye
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Laurentijn Tilleman
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Ann-Sophie Vander Plaetsen
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Senne Cornelis
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium.
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Deleye L, Dheedene A, De Coninck D, Sante T, Christodoulou C, Heindryckx B, Van den Abbeel E, De Sutter P, Deforce D, Menten B, Van Nieuwerburgh F. Shallow whole genome sequencing is well suited for the detection of chromosomal aberrations in human blastocysts. Fertil Steril 2015; 104:1276-85.e1. [DOI: 10.1016/j.fertnstert.2015.07.1144] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 06/24/2015] [Accepted: 07/06/2015] [Indexed: 01/27/2023]
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Deleye L, De Coninck D, Christodoulou C, Sante T, Dheedene A, Heindryckx B, Van den Abbeel E, De Sutter P, Menten B, Deforce D, Van Nieuwerburgh F. Whole genome amplification with SurePlex results in better copy number alteration detection using sequencing data compared to the MALBAC method. Sci Rep 2015; 5:11711. [PMID: 26122179 PMCID: PMC4485032 DOI: 10.1038/srep11711] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 06/03/2015] [Indexed: 11/09/2022] Open
Abstract
Current whole genome amplification (WGA) methods lead to amplification bias resulting in over- and under-represented regions in the genome. Nevertheless, certain WGA methods, such as SurePlex and subsequent arrayCGH analysis, make it possible to detect copy number alterations (CNAs) at a 10 Mb resolution. A more uniform WGA combined with massive parallel sequencing (MPS), however, could allow detection at higher resolution and lower cost. Recently, MALBAC, a new WGA method, claims unparalleled performance. Here, we compared the well-established SurePlex and MALBAC WGA for their ability to detect CNAs in MPS generated data and, in addition, compared PCR-free MPS library preparation with the standard enrichment PCR library preparation. Results showed that SurePlex amplification led to more uniformity across the genome, allowing for a better CNA detection with less false positives compared to MALBAC amplified samples. An even more uniform coverage was observed in samples following a PCR-free library preparation. In general, the combination of SurePlex and MPS led to the same chromosomal profile compared to a reference arrayCGH from unamplified genomic DNA, underlining the large potential of MPS techniques in CNA detection from a limited number of DNA material.
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Affiliation(s)
- Lieselot Deleye
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Dieter De Coninck
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | | | - Tom Sante
- Center for Medical Genetics, Ghent University, De Pintelaan 185, 9000 Ghent, Belgium
| | - Annelies Dheedene
- Center for Medical Genetics, Ghent University, De Pintelaan 185, 9000 Ghent, Belgium
| | - Björn Heindryckx
- Department for Reproductive Medicine, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium
| | - Etienne Van den Abbeel
- Department for Reproductive Medicine, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium
| | - Petra De Sutter
- Department for Reproductive Medicine, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics, Ghent University, De Pintelaan 185, 9000 Ghent, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
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Abstract
With the passive anterior rhinomanometry technique, it was shown that children aged 3 to 6 years did not have an alternating nasal cycle. However, during a 61/4-hour period, there was a quite regular pattern of fluctuations of the nasal resistance. Important fluctuations of the nasal resistance in the left and right nasal cavity are happening in the same sense; we could call it "solidary movements" or "solidary cycle." This means that the total nasal resistance in these children is not at all constant during the day. The mean duration of such a "cycle" is 57 minutes, and the mean amplitude is 16.0 mm H2O for the left and right nasal cavity and 6.5 mm H2O for the total nasal resistance.
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