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Zorzi F, Bonfadini S, Aloisio L, Moschetta M, Storti F, Simoni F, Lanzani G, Criante L. Optofluidic Flow Cytometer with In-Plane Spherical Mirror for Signal Enhancement. SENSORS (BASEL, SWITZERLAND) 2023; 23:9191. [PMID: 38005576 PMCID: PMC10675696 DOI: 10.3390/s23229191] [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: 09/26/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023]
Abstract
Statistical analysis of the properties of single microparticles, such as cells, bacteria or plastic slivers, has attracted increasing interest in recent years. In this regard, field flow cytometry is considered the gold standard technique, but commercially available instruments are bulky, expensive, and not suitable for use in point-of-care (PoC) testing. Microfluidic flow cytometers, on the other hand, are small, cheap and can be used for on-site analyses. However, in order to detect small particles, they require complex geometries and the aid of external optical components. To overcome these limitations, here, we present an opto-fluidic flow cytometer with an integrated 3D in-plane spherical mirror for enhanced optical signal collection. As a result, the signal-to-noise ratio is increased by a factor of six, enabling the detection of particle sizes down to 1.5 µm. The proposed optofluidic detection scheme enables the simultaneous collection of particle fluorescence and scattering using a single optical fiber, which is crucial to easily distinguishing particle populations with different optical properties. The devices have been fully characterized using fluorescent polystyrene beads of different sizes. As a proof of concept for potential real-world applications, signals from fluorescent HEK cells and Escherichia coli bacteria were analyzed.
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Affiliation(s)
- Filippo Zorzi
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia, Via Rubattino 81, 20134 Milan, Italy; (F.Z.); (S.B.); (L.A.); (M.M.); (F.S.); (G.L.)
- Department of Physics, Politecnico di Milano, Piazza Leonardo da Vinci, 32, 20133 Milan, Italy
| | - Silvio Bonfadini
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia, Via Rubattino 81, 20134 Milan, Italy; (F.Z.); (S.B.); (L.A.); (M.M.); (F.S.); (G.L.)
| | - Ludovico Aloisio
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia, Via Rubattino 81, 20134 Milan, Italy; (F.Z.); (S.B.); (L.A.); (M.M.); (F.S.); (G.L.)
- Department of Physics, Politecnico di Milano, Piazza Leonardo da Vinci, 32, 20133 Milan, Italy
| | - Matteo Moschetta
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia, Via Rubattino 81, 20134 Milan, Italy; (F.Z.); (S.B.); (L.A.); (M.M.); (F.S.); (G.L.)
| | - Filippo Storti
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia, Via Rubattino 81, 20134 Milan, Italy; (F.Z.); (S.B.); (L.A.); (M.M.); (F.S.); (G.L.)
| | - Francesco Simoni
- Università Politecnica delle Marche, 60131 Ancona, Italy;
- Institute of Applied Sciences and Intelligent Systems, Consiglio Nazionale delle Ricerche (CNR), 80072 Pozzuoli, Italy
| | - Guglielmo Lanzani
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia, Via Rubattino 81, 20134 Milan, Italy; (F.Z.); (S.B.); (L.A.); (M.M.); (F.S.); (G.L.)
| | - Luigino Criante
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia, Via Rubattino 81, 20134 Milan, Italy; (F.Z.); (S.B.); (L.A.); (M.M.); (F.S.); (G.L.)
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Källberg J, Xiao W, Van Assche D, Baret JC, Taly V. Frontiers in single cell analysis: multimodal technologies and their clinical perspectives. LAB ON A CHIP 2022; 22:2403-2422. [PMID: 35703438 DOI: 10.1039/d2lc00220e] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Single cell multimodal analysis is at the frontier of single cell research: it defines the roles and functions of distinct cell types through simultaneous analysis to provide unprecedented insight into cellular processes. Current single cell approaches are rapidly moving toward multimodal characterizations. It replaces one-dimensional single cell analysis, for example by allowing for simultaneous measurement of transcription and post-transcriptional regulation, epigenetic modifications and/or surface protein expression. By providing deeper insights into single cell processes, multimodal single cell analyses paves the way to new understandings in various cellular processes such as cell fate decisions, physiological heterogeneity or genotype-phenotype linkages. At the forefront of this, microfluidics is key for high-throughput single cell analysis. Here, we present an overview of the recent multimodal microfluidic platforms having a potential in biomedical research, with a specific focus on their potential clinical applications.
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Affiliation(s)
- Julia Källberg
- Centre de Recherche des Cordeliers, INSERM, CNRS, Université Paris Cité, Sorbonne Université, USPC, Equipe labellisée Ligue Nationale contre le cancer, Paris, France.
| | - Wenjin Xiao
- Centre de Recherche des Cordeliers, INSERM, CNRS, Université Paris Cité, Sorbonne Université, USPC, Equipe labellisée Ligue Nationale contre le cancer, Paris, France.
| | - David Van Assche
- University of Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR 5031, Pessac 33600, France.
| | - Jean-Christophe Baret
- University of Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR 5031, Pessac 33600, France.
- Institut Universitaire de France, Paris 75005, France
| | - Valerie Taly
- Centre de Recherche des Cordeliers, INSERM, CNRS, Université Paris Cité, Sorbonne Université, USPC, Equipe labellisée Ligue Nationale contre le cancer, Paris, France.
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Patel YM, Jain S, Singh AK, Khare K, Ahlawat S, Bahga SS. An inexpensive microfluidic device for three-dimensional hydrodynamic focusing in imaging flow cytometry. BIOMICROFLUIDICS 2020; 14:064110. [PMID: 33343784 PMCID: PMC7738198 DOI: 10.1063/5.0033291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 11/13/2020] [Indexed: 06/12/2023]
Abstract
We present design, characterization, and testing of an inexpensive, sheath-flow based microfluidic device for three-dimensional (3D) hydrodynamic focusing of cells in imaging flow cytometry. In contrast to other 3D sheathing devices, our device hydrodynamically focuses the cells in a single-file near the bottom wall of the microchannel that allows imaging cells with high magnification and low working distance objectives, without the need for small device dimensions. The relatively large dimensions of the microchannels enable easy fabrication using less-precise fabrication techniques, and the simplicity of the device design avoids the need for tedious alignment of various layers. We have characterized the performance of the device with 3D numerical simulations and validated these simulations with experiments of hydrodynamic focusing of a fluorescently dyed sample fluid. The simulations show that the width and the height of the 3D focused sample stream can be controlled independently by varying the heights of main and side channels of the device, and the flow rates of sample and sheath fluids. Based on simulations, we also provide useful guidelines for choosing the device dimensions and flow rates for focusing cells of a particular size. Thereafter, we demonstrate the applicability of our device for imaging a large number of RBCs using brightfield microscopy. We also discuss the choice of the region of interest and camera frame rate so as to image each cell individually in our device. The design of our microfluidic device makes it equally applicable for imaging cells of different sizes using various other imaging techniques such as phase-contrast and fluorescence microscopy.
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Affiliation(s)
- Yogesh M. Patel
- Department of Mechanical Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Sanidhya Jain
- Department of Mechanical Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Abhishek Kumar Singh
- Department of Mechanical Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Kedar Khare
- Department of Physics, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Sarita Ahlawat
- Phase Laboratories Pvt. Ltd., Technology Based Incubation Unit, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Supreet Singh Bahga
- Department of Mechanical Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
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Self-Learning Microfluidic Platform for Single-Cell Imaging and Classification in Flow. MICROMACHINES 2019; 10:mi10050311. [PMID: 31075890 PMCID: PMC6563144 DOI: 10.3390/mi10050311] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 05/06/2019] [Indexed: 02/07/2023]
Abstract
Single-cell analysis commonly requires the confinement of cell suspensions in an analysis chamber or the precise positioning of single cells in small channels. Hydrodynamic flow focusing has been broadly utilized to achieve stream confinement in microchannels for such applications. As imaging flow cytometry gains popularity, the need for imaging-compatible microfluidic devices that allow for precise confinement of single cells in small volumes becomes increasingly important. At the same time, high-throughput single-cell imaging of cell populations produces vast amounts of complex data, which gives rise to the need for versatile algorithms for image analysis. In this work, we present a microfluidics-based platform for single-cell imaging in-flow and subsequent image analysis using variational autoencoders for unsupervised characterization of cellular mixtures. We use simple and robust Y-shaped microfluidic devices and demonstrate precise 3D particle confinement towards the microscope slide for high-resolution imaging. To demonstrate applicability, we use these devices to confine heterogeneous mixtures of yeast species, brightfield-image them in-flow and demonstrate fully unsupervised, as well as few-shot classification of single-cell images with 88% accuracy.
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Rane AS, Rutkauskaite J, deMello A, Stavrakis S. High-Throughput Multi-parametric Imaging Flow Cytometry. Chem 2017. [DOI: 10.1016/j.chempr.2017.08.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Qin LR, Zhou Y, Deng XF, Li HT, Zang N, He M. Identification of genes related to hepatocellular carcinoma metastasis by a combined transcriptomics and proteomics approach. Shijie Huaren Xiaohua Zazhi 2015; 23:2050-2057. [DOI: 10.11569/wcjd.v23.i13.2050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To screening key genes related to hepatocellular carcinoma (HCC) metastasis by high-throughput transcriptomics sequencing and serum proteomics.
METHODS: Differentially expressed genes between liver cancer cells Smmc-7721 and normal liver cells L-02 were analyzed by Ion Proton™ high-throughput sequencing. Bioinformatics methods were used to perform GO annotation, clustering and enrichment analysis. Ten serum samples from HCC patients and 10 normal serum samples were recruited to detect the differential protein expression by isobaric tags for relative and absolute quantitation (iTRAQ) and matrix-assisted laser desorption/ionization tandem time of flight mass spectrometry (MALDI-TOF/MS). The transcriptomics data and serum proteomics data were analyzed together to screen key genes related to HCC metastasis. Then, a screened key gene was verified by immunohistochemistry in 76 HCC and adjacent tissues.
RESULTS: A total of 618 differentially expressed genes (DEGs) in liver cancer cells were identified by transcriptome sequencing, and the gene functions were enriched in 14 terms, including metastasis process, transcription and REDOX process, among which metastasis process owned the most DEGs [15.05% (93/618)]. The proteomics data showed that a total of 69 differentially expressed proteins in HCC were detected, including 33 up-regulated and 36 down-regulated ones. Combination analysis found three common factors in transcriptomics and proteomics, among which heat shock protein 90 AA1 (HSP90AA1) was up-regulated in HCC and presented the most significant ratio. According to the immunohistochemical results, the strongly positive rates of HSP90α in HCC with portal vein metastasis and without were 66.7% (16/24) and 25% (13/52), respectively (P < 0.005). HSP90α was overexpressed in HCC with portal vein metastasis.
CONCLUSION: Transcriptomics and proteomics analysis revealed that HSP90AA1 might be a key gene related to HCC metastasis.
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Gholami M, Bekele WA, Schondelmaier J, Snowdon RJ. A tailed PCR procedure for cost-effective, two-order multiplex sequencing of candidate genes in polyploid plants. PLANT BIOTECHNOLOGY JOURNAL 2012; 10:635-45. [PMID: 22489678 DOI: 10.1111/j.1467-7652.2012.00696.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Complex polyploid crop genomes can be recalcitrant towards conventional DNA sequencing approaches for allele mining in candidate genes for valuable traits. In the past, this has greatly complicated the transfer of knowledge on promising candidate genes from model plants to even closely related polyploid crops. Next-generation sequencing offers diverse solutions to overcome such difficulties. Here, we present a method for multiplexed 454 sequencing in gene-specific PCR amplicons that can simultaneously address multiple homologues of given target genes. We devised a simple two-step PCR procedure employing a set of barcoded M13/T7 universal fusion primers that enable a cost-effective and efficient amplification of large numbers of target gene amplicons. Sequencing-ready amplicons are generated that can be simultaneously sequenced in pools comprising multiple amplicons from multiple genotypes. High-depth sequencing allows resolution of the resulting sequence reads into contigs representing multiple homologous loci, with only insignificant off-target capture of paralogues or PCR artefacts. In a case study, the procedure was tested in the complex polyploid genome of Brassica napus for a set of nine genes identified in Arabidopsis as candidates for regulation of seed development and oil content. Up to six copies of these genes were expected in B. napus. SNP discovery was performed by pooled multiplex sequencing of 30 amplicons in 20 diverse B. napus accessions with interesting trait variation for oil content, providing a basis for comparative mapping to relevant quantitative trait loci and for subsequent marker-assisted breeding.
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Affiliation(s)
- Mahmood Gholami
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany Saaten-Union Biotec GmbH, Leopoldshoehe, Germany
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