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Special Issue "Single Cell Technology"

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry, Molecular and Cellular Biology".

Deadline for manuscript submissions: 20 October 2018

Special Issue Editors

Guest Editor
Assis. Prof. Dr. Tuhin Subhra Santra

Department of Engineering Design, Indian Institute of Technology Madras, Chennai, 600036, India
Website | E-Mail
Interests: MEMS; Bio-NEMS; single cell technology; biomedical micro/nano devices; micro/nanofluidics; nanomedicine
Guest Editor
Prof. Fan-Gang Tseng

Department of Engineering and System Science, National Tsing-Hua University, Hsinchu 30013, Taiwan
Website | E-Mail
Interests: MEMS/NEMS; microfluidics; 3D tissue culture; electrochemical sensors; nanotechnology in biomedical application

Special Issue Information

Dear Colleagues,

The cell is the most fundamental building block in our body and it is presently a great challenge in cell biology to understand cell-to-cell responses, and how an individual cell delivers its information to others. The average ensemble measurement of cells cannot provide information regarding the detailed behaviors of any individual cell; however, each cell in heterogeneous populations has its own unique behavior and it has different responses, even after treatment with the same reagents or drugs as other cells. On the other hand, single cell sequencing (SCS) is able to empirically infer driver mutations and to map sequential mutation events during cancer development. The integration of single-cell genomics and transcriptomics is able to provide functional consequences of mutations and the copy number variations of cells. Thus, single cell technology (SCT) has the power to understand fundamental cell biology in embryonic development, detailed knowledge of cell lineage trees in higher organisms, to dissect tumor heterogeneity and disease, etc. Recently, the development of micro/nanofluidic technologies have enabled the characterization of a single cell in the micro/nanoscale environments with a massively parallel platform, which can distinguish cell-to-cell heterogeneity via tracking responses over time. The devices are, not only useful for cell manipulation, isolation, separation, and analysis, but are also able to control cellular parameters at the single cell level.

This Special Issue will invite the latest research articles and reviews dealing with SCT, and the role of SCT in omics. Applications and future prospects, with their advantages and limitations, are also welcome.

Dr. Tuhin Subhra Santra
Prof. Dr. Fan-Gang Tseng
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Single cells interaction, perturbation, cultivation, cellular heterogeneity
  • single cell in system biology
  • single cell cytometry
  • micro/nano fluidic devices for single cell analysis
  • single cell manipulation, separation, detection
  • single cell genomics, proteomics, transcriptomics, metabolomics and fluxomics
  • single cell diagnostics and imaging

Related Special Issue

Published Papers (5 papers)

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Research

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Open AccessCommunication Localization Microscopy of Actin Cytoskeleton in Human Platelets
Int. J. Mol. Sci. 2018, 19(4), 1150; https://doi.org/10.3390/ijms19041150
Received: 23 February 2018 / Revised: 3 April 2018 / Accepted: 5 April 2018 / Published: 11 April 2018
PDF Full-text (6853 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Here, we measure the actin cytoskeleton arrangement of different morphological states of human platelets using a new protocol for photo-switching of rhodamine class fluorophores. A new medium composition was established for imaging the cytoskeleton using Alexa Fluor 488 conjugated to phalloidin. Morphological states
[...] Read more.
Here, we measure the actin cytoskeleton arrangement of different morphological states of human platelets using a new protocol for photo-switching of rhodamine class fluorophores. A new medium composition was established for imaging the cytoskeleton using Alexa Fluor 488 conjugated to phalloidin. Morphological states of platelets bound to a glass substrate are visualized and quantified by two-dimensional localization microscopy at nanoscopic resolution. Marker-less drift correction yields localization of individual Alexa 488 conjugated to phalloidin with a positional accuracy of 12 nm. Full article
(This article belongs to the Special Issue Single Cell Technology)
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Open AccessArticle A Novel Workflow to Enrich and Isolate Patient-Matched EpCAMhigh and EpCAMlow/negative CTCs Enables the Comparative Characterization of the PIK3CA Status in Metastatic Breast Cancer
Int. J. Mol. Sci. 2017, 18(9), 1885; https://doi.org/10.3390/ijms18091885
Received: 14 July 2017 / Revised: 21 August 2017 / Accepted: 25 August 2017 / Published: 31 August 2017
PDF Full-text (2568 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Circulating tumor cells (CTCs), potential precursors of most epithelial solid tumors, are mainly enriched by epithelial cell adhesion molecule (EpCAM)-dependent technologies. Hence, these approaches may overlook mesenchymal CTCs, considered highly malignant. Our aim was to establish a workflow to enrich and isolate patient-matched
[...] Read more.
Circulating tumor cells (CTCs), potential precursors of most epithelial solid tumors, are mainly enriched by epithelial cell adhesion molecule (EpCAM)-dependent technologies. Hence, these approaches may overlook mesenchymal CTCs, considered highly malignant. Our aim was to establish a workflow to enrich and isolate patient-matched EpCAMhigh and EpCAMlow/negative CTCs within the same blood samples, and to investigate the phosphatidylinositol 3-kinase catalytic subunit alpha (PIK3CA) mutational status within single CTCs. We sequentially processed metastatic breast cancer (MBC) blood samples via CellSearch® (EpCAM-based) and via Parsortix™ (size-based) systems. After enrichment, cells captured in Parsortix™ cassettes were stained in situ for nuclei, cytokeratins, EpCAM and CD45. Afterwards, sorted cells were isolated via CellCelector™ micromanipulator and their genomes were amplified. Lastly, PIK3CA mutational status was analyzed by combining an amplicon-based approach with Sanger sequencing. In 54% of patients′ blood samples both EpCAMhigh and EpCAMlow/negative cells were identified and successfully isolated. High genomic integrity was observed in 8% of amplified genomes of EpCAMlow/negative cells vs. 28% of EpCAMhigh cells suggesting an increased apoptosis in the first CTC-subpopulation. Furthermore, PIK3CA hotspot mutations were detected in both EpCAMhigh and EpCAMlow/negative CTCs. Our workflow is suitable for single CTC analysis, permitting—for the first time—assessment of the heterogeneity of PIK3CA mutational status within patient-matched EpCAMhigh and EpCAMlow/negative CTCs. Full article
(This article belongs to the Special Issue Single Cell Technology)
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Graphical abstract

Open AccessArticle The Instrumentation of a Microfluidic Analyzer Enabling the Characterization of the Specific Membrane Capacitance, Cytoplasm Conductivity, and Instantaneous Young’s Modulus of Single Cells
Int. J. Mol. Sci. 2017, 18(6), 1158; https://doi.org/10.3390/ijms18061158
Received: 16 April 2017 / Revised: 23 May 2017 / Accepted: 25 May 2017 / Published: 19 June 2017
PDF Full-text (1826 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
This paper presents the instrumentation of a microfluidic analyzer enabling the characterization of single-cell biophysical properties, which includes seven key components: a microfluidic module, a pressure module, an imaging module, an impedance module, two LabVIEW platforms for instrument operation and raw data processing,
[...] Read more.
This paper presents the instrumentation of a microfluidic analyzer enabling the characterization of single-cell biophysical properties, which includes seven key components: a microfluidic module, a pressure module, an imaging module, an impedance module, two LabVIEW platforms for instrument operation and raw data processing, respectively, and a Python code for data translation. Under the control of the LabVIEW platform for instrument operation, the pressure module flushes single cells into the microfluidic module with raw biophysical parameters sampled by the imaging and impedance modules and processed by the LabVIEW platform for raw data processing, which were further translated into intrinsic cellular biophysical parameters using the code developed in Python. Based on this system, specific membrane capacitance, cytoplasm conductivity, and instantaneous Young’s modulus of three cell types were quantified as 2.76 ± 0.57 μF/cm2, 1.00 ± 0.14 S/m, and 3.79 ± 1.11 kPa for A549 cells (ncell = 202); 1.88 ± 0.31 μF/cm2, 1.05 ± 0.16 S/m, and 3.74 ± 0.75 kPa for 95D cells (ncell = 257); 2.11 ± 0.38 μF/cm2, 0.87 ± 0.11 S/m, and 5.39 ± 0.89 kPa for H460 cells (ncell = 246). As a semi-automatic instrument with a throughput of roughly 1 cell per second, this prototype instrument can be potentially used for the characterization of cellular biophysical properties. Full article
(This article belongs to the Special Issue Single Cell Technology)
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Review

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Open AccessReview Platforms for Single-Cell Collection and Analysis
Int. J. Mol. Sci. 2018, 19(3), 807; https://doi.org/10.3390/ijms19030807
Received: 1 February 2018 / Revised: 1 March 2018 / Accepted: 6 March 2018 / Published: 11 March 2018
Cited by 1 | PDF Full-text (513 KB) | HTML Full-text | XML Full-text
Abstract
Single-cell analysis has become an established method to study cell heterogeneity and for rare cell characterization. Despite the high cost and technical constraints, applications are increasing every year in all fields of biology. Following the trend, there is a tremendous development of tools
[...] Read more.
Single-cell analysis has become an established method to study cell heterogeneity and for rare cell characterization. Despite the high cost and technical constraints, applications are increasing every year in all fields of biology. Following the trend, there is a tremendous development of tools for single-cell analysis, especially in the RNA sequencing field. Every improvement increases sensitivity and throughput. Collecting a large amount of data also stimulates the development of new approaches for bioinformatic analysis and interpretation. However, the essential requirement for any analysis is the collection of single cells of high quality. The single-cell isolation must be fast, effective, and gentle to maintain the native expression profiles. Classical methods for single-cell isolation are micromanipulation, microdissection, and fluorescence-activated cell sorting (FACS). In the last decade several new and highly efficient approaches have been developed, which not just supplement but may fully replace the traditional ones. These new techniques are based on microfluidic chips, droplets, micro-well plates, and automatic collection of cells using capillaries, magnets, an electric field, or a punching probe. In this review we summarize the current methods and developments in this field. We discuss the advantages of the different commercially available platforms and their applicability, and also provide remarks on future developments. Full article
(This article belongs to the Special Issue Single Cell Technology)
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Open AccessReview Recent Advances in Experimental Whole Genome Haplotyping Methods
Int. J. Mol. Sci. 2017, 18(9), 1944; https://doi.org/10.3390/ijms18091944
Received: 3 August 2017 / Revised: 1 September 2017 / Accepted: 5 September 2017 / Published: 11 September 2017
PDF Full-text (2359 KB) | HTML Full-text | XML Full-text
Abstract
Haplotype plays a vital role in diverse fields; however, the sequencing technologies cannot resolve haplotype directly. Pioneers demonstrated several approaches to resolve haplotype in the early years, which was extensively reviewed. Since then, numerous methods have been developed recently that have significantly improved
[...] Read more.
Haplotype plays a vital role in diverse fields; however, the sequencing technologies cannot resolve haplotype directly. Pioneers demonstrated several approaches to resolve haplotype in the early years, which was extensively reviewed. Since then, numerous methods have been developed recently that have significantly improved phasing performance. Here, we review experimental methods that have emerged mainly over the past five years, and categorize them into five classes according to their maximum scale of contiguity: (i) encapsulation, (ii) 3D structure capture and construction, (iii) compartmentalization, (iv) fluorography, (v) long-read sequencing. Several subsections of certain methods are attached to each class as instances. We also discuss the relative advantages and disadvantages of different classes and make comparisons among representative methods of each class. Full article
(This article belongs to the Special Issue Single Cell Technology)
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