Single Cell Analysis of Complex Biological Systems

A special issue of Cells (ISSN 2073-4409).

Deadline for manuscript submissions: closed (31 October 2021) | Viewed by 8330

Special Issue Editors


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Guest Editor
Group Leader, Tumour Development—The Kinghorn Cancer Centre, Garvan Institute of Medical Research; Conjoint Senior Lecturer—St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales Sydney; Senior Research Fellow—Institute for Biomedical Materials & Devices (IBMD), School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, Sydney, Australia
Interests: single-cell genomics; high-dimensional cell characterization; breast cancer and mammary development; metastasis; tumour immunobiology and immunotherapy; tumour infiltrated immunosuppressive myeloid cells populations; tissue engineering

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Guest Editor
Team Leader—Cancer Epigenetic Biology and Therapeutics, Personalised Medicine, Children’s Cancer Institute; Conjoint Senior Lecturer—School of Women's and Children's Health, Faculty of Medicine, University of New South Wales Sydney, Sydney, Australia
Interests: to identify the key epigenetic factors that drive carcinogenesis and to study the underlying molecular mechanisms; to use next-generation sequencing methodologies, single cell transcriptomics and epigenomics and bioinformatics interpretation of genome-wide data to answer biological related questions; to apply this knowledge for the design of new epigenetic-based therapies

Special Issue Information

High-dimensional single-cell analysis enables a deep understanding of the cellular and molecular mechanisms of complex biological systems. Recent technological advances have made it possible to unravel the genome, epigenome, transcriptome, and proteome one cell at the time. This technical capacity has driven a parallel revolution on the development of new computational frameworks to rapidly analyze, visualize, and integrate single-cell data, enabling a multi-omic characterization of a single cell. A major milestone on the single-cell omics revolution was achieved with the development of highly parallel single-cell transcriptomics, transforming and fast-pacing the study of biological processes, breaking paradigms and uncovering new cell types. Another important milestone developed in this field was the capacity for high-dimensional analysis of single cells while preserving the tissue context, producing detailed histological fingerprints of cellular niches.

A diverse range of single-cell technologies have been progressively adopted by the scientific community, and many of those are now routinely used to understand the function and cell composition of normal tissue, including developmental stages and disease. This Special Issue is intended to take a snapshot of this fast-moving field, inviting reviews and original research manuscripts of any modality of single-cell analysis in all aspects of biology and medicine using mammalian and non-mammalian cellular systems, animal models of development and disease, and clinical cohorts. As guest editors of this Special Issue on “Single-Cell Analysis of Complex Biological Systems”, we encourage submissions of descriptive cell atlas-based studies, in depth mechanistic studies, new methodologies, computational approaches or meta-analyses of existing single-cell resolution data.

Dr. David Gallego-Ortega
Dr. Fatima Valdes Mora
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. Cells is an international peer-reviewed open access semimonthly 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 transcriptomics
  • single-cell genomics
  • single-cell epigenomics
  • multi-omic analysis
  • computational methods
  • scRNA-seq
  • scATAC-seq
  • CITE-seq
  • CyTOF
  • mass cytometry
  • spatial transcriptomics
  • high-dimensional cellular analysis

Published Papers (2 papers)

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Research

23 pages, 18005 KiB  
Article
Multidimensional Single-Nuclei RNA-Seq Reconstruction of Adipose Tissue Reveals Adipocyte Plasticity Underlying Thermogenic Response
by Carlos Alberto Oliveira Biagi, Jr., Sarah Santiloni Cury, Cleidson Pádua Alves, Nabil Rabhi, Wilson Araujo Silva, Jr., Stephen R. Farmer, Robson Francisco Carvalho and Miguel Luiz Batista, Jr.
Cells 2021, 10(11), 3073; https://doi.org/10.3390/cells10113073 - 08 Nov 2021
Cited by 9 | Viewed by 4698
Abstract
Adipose tissue has been classified based on its morphology and function as white, brown, or beige/brite. It plays an essential role as a regulator of systemic metabolism through paracrine and endocrine signals. Recently, multiple adipocyte subtypes have been revealed using RNA sequencing technology, [...] Read more.
Adipose tissue has been classified based on its morphology and function as white, brown, or beige/brite. It plays an essential role as a regulator of systemic metabolism through paracrine and endocrine signals. Recently, multiple adipocyte subtypes have been revealed using RNA sequencing technology, going beyond simply defined morphology but also by their cellular origin, adaptation to metabolic stress, and plasticity. Here, we performed an in-depth analysis of publicly available single-nuclei RNAseq from adipose tissue and utilized a workflow template to characterize adipocyte plasticity, heterogeneity, and secretome profiles. The reanalyzed dataset led to the identification of different subtypes of adipocytes including three subpopulations of thermogenic adipocytes, and provided a characterization of distinct transcriptional profiles along the adipocyte trajectory under thermogenic challenges. This study provides a useful resource for further investigations regarding mechanisms related to adipocyte plasticity and trans-differentiation. Full article
(This article belongs to the Special Issue Single Cell Analysis of Complex Biological Systems)
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12 pages, 4763 KiB  
Article
Highly Sensitive and Multiplexed In Situ RNA Profiling with Cleavable Fluorescent Tyramide
by Lu Xiao, Joshua Labaer and Jia Guo
Cells 2021, 10(6), 1277; https://doi.org/10.3390/cells10061277 - 21 May 2021
Cited by 6 | Viewed by 2962
Abstract
Understanding the composition, regulation, and function of complex biological systems requires tools that quantify multiple transcripts at their native cellular locations. However, the current multiplexed RNA imaging technologies are limited by their relatively low sensitivity or specificity, which hinders their applications in studying [...] Read more.
Understanding the composition, regulation, and function of complex biological systems requires tools that quantify multiple transcripts at their native cellular locations. However, the current multiplexed RNA imaging technologies are limited by their relatively low sensitivity or specificity, which hinders their applications in studying highly autofluorescent tissues, such as formalin-fixed paraffin-embedded (FFPE) tissues. To address this issue, here we develop a multiplexed in situ RNA profiling approach with a high sensitivity and specificity. In this approach, transcripts are first hybridized by target-specific oligonucleotide probes in pairs. Only when these two independent probes hybridize to the target in tandem will the subsequent signal amplification by oligonucleotide hybridization occur. Afterwards, horseradish peroxidase (HRP) is applied to further amplify the signal and stain the target with cleavable fluorescent tyramide (CFT). After imaging, the fluorophores are chemically cleaved and the hybridized probes are stripped by DNase and formamide. Through cycles of RNA staining, fluorescence imaging, signal cleavage, and probe stripping, many different RNA species can be profiled at the optical resolution. In applying this approach, we demonstrated that multiplexed in situ RNA analysis can be successfully achieved in both fixed, frozen, and FFPE tissues. Full article
(This article belongs to the Special Issue Single Cell Analysis of Complex Biological Systems)
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