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9.4
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Biomolecules
Special Issues
Reality and Perspectives for Single Cell RNA Sequencing
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Reality and Perspectives for Single Cell RNA Sequencing

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Molecular Genetics".

Deadline for manuscript submissions: closed (30 November 2021) | Viewed by 21288

Special Issue Editors

Prof. Hae-Ock Lee

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Guest Editor
College of Medicine, The Catholic University of Korea, Seoul, Korea
Interests: single cell genomics; cancer; stromal and immune microenvironment in health and disease
Prof. Dr. Yeun-Jun Chung

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Guest Editor
1. Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 03083, Republic of Korea
2. Precision Medicine Research Center, Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul 03083, Republic of Korea
Interests: precision medicine; single cell genomics; cancer genomics; genome variation

Special Issue Information

Dear Colleagues,

Although recent large-scale transcriptomic studies have revealed aberrant regulatory pathways and disease subtypes of human cancers, most of these studies measure the expression profiles of tumors in bulk average. However, substantial evidence indicates that intratumoral heterogeneity among malignant and non-malignant cells, and their interactions within the tumor microenvironment are critical to understand diverse aspects of tumor biology. Transcriptomes of thousands of cells can be massively parallel characterized by the development of recent technology in single-cell RNA sequencing. Single-cell RNA sequencing would help to dissect tumor complexity by characterizing the molecular landscape by cellular components, which could deepen our understanding of tumor heterogeneity and the microenvironment. We invite authors to submit research or review articles describing recent findings in single-cell RNA sequencing in cancer. The following are the main interests in this Special Issue: 1) What do we expect from single-cell level genomics? (expectations and frustrations) 2) What can we achieve with single-cell level genomics, and how? (current technology review and perspectives) 3) What is the best way of data sharing for single-cell RNA sequencing?

Prof. Hae-Ock Lee
Prof. Yeun-Jun Chung
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 submissions that pass pre-check are 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. Biomolecules 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 2700 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-cell sequencing
  • cancer
  • tumor microenviroment
  • tumor heterogeneity sequencing
  • bioinformatics

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Published Papers (3 papers)

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Review

25 pages, 1155 KiB  
Review
Deciphering Cardiac Biology and Disease by Single-Cell Transcriptomic Profiling
by Le Wang, Shengshou Hu and Bingying Zhou
Biomolecules 2022, 12(4), 566; https://doi.org/10.3390/biom12040566 - 12 Apr 2022
Cited by 4 | Viewed by 5646
Abstract
By detecting minute molecular changes in hundreds to millions of single cells, single-cell RNA sequencing allows for the comprehensive characterization of the diversity and dynamics of cells in the heart. Our understanding of the heart has been transformed through the recognition of cellular [...] Read more.
By detecting minute molecular changes in hundreds to millions of single cells, single-cell RNA sequencing allows for the comprehensive characterization of the diversity and dynamics of cells in the heart. Our understanding of the heart has been transformed through the recognition of cellular heterogeneity, the construction of regulatory networks, the building of lineage trajectories, and the mapping of intercellular crosstalk. In this review, we introduce cardiac progenitors and their transcriptional regulation during embryonic development, highlight cellular heterogeneity and cell subtype functions in cardiac health and disease, and discuss insights gained from the study of pluripotent stem-cell-derived cardiomyocytes. Full article
(This article belongs to the Special Issue Reality and Perspectives for Single Cell RNA Sequencing)
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17 pages, 1962 KiB  
Review
Clinical Perspectives of Single-Cell RNA Sequencing
by Nayoung Kim, Hye Hyeon Eum and Hae-Ock Lee
Biomolecules 2021, 11(8), 1161; https://doi.org/10.3390/biom11081161 - 6 Aug 2021
Cited by 13 | Viewed by 6649
Abstract
The ability of single-cell genomics to resolve cellular heterogeneity is highly appreciated in cancer and is being exploited for precision medicine. In the recent decade, we have witnessed the incorporation of cancer genomics into the clinical decision-making process for molecular-targeted therapies. Compared with [...] Read more.
The ability of single-cell genomics to resolve cellular heterogeneity is highly appreciated in cancer and is being exploited for precision medicine. In the recent decade, we have witnessed the incorporation of cancer genomics into the clinical decision-making process for molecular-targeted therapies. Compared with conventional genomics, which primarily focuses on the specific and sensitive detection of the molecular targets, single-cell genomics addresses intratumoral heterogeneity and the microenvironmental components impacting the treatment response and resistance. As an exploratory tool, single-cell genomics provides an unprecedented opportunity to improve the diagnosis, monitoring, and treatment of cancer. The results obtained upon employing bulk cancer genomics indicate that single-cell genomics is at an early stage with respect to exploration of clinical relevance and requires further innovations to become a widely utilized technology in the clinic. Full article
(This article belongs to the Special Issue Reality and Perspectives for Single Cell RNA Sequencing)
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20 pages, 3534 KiB  
Review
Introduction to Single-Cell DNA Methylation Profiling Methods
by Jongseong Ahn, Sunghoon Heo, Jihyun Lee and Duhee Bang
Biomolecules 2021, 11(7), 1013; https://doi.org/10.3390/biom11071013 - 10 Jul 2021
Cited by 39 | Viewed by 7941
Abstract
DNA methylation is an epigenetic mechanism that is related to mammalian cellular differentiation, gene expression regulation, and disease. In several studies, DNA methylation has been identified as an effective marker to identify differences between cells. In this review, we introduce single-cell DNA-methylation profiling [...] Read more.
DNA methylation is an epigenetic mechanism that is related to mammalian cellular differentiation, gene expression regulation, and disease. In several studies, DNA methylation has been identified as an effective marker to identify differences between cells. In this review, we introduce single-cell DNA-methylation profiling methods, including experimental strategies and approaches to computational data analysis. Furthermore, the blind spots of the basic analysis and recent alternatives are briefly described. In addition, we introduce well-known applications and discuss future development. Full article
(This article belongs to the Special Issue Reality and Perspectives for Single Cell RNA Sequencing)
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