Article
Biochemistry & Molecular Biology
Xiaoying Shi, Zhiguang Yu, Pengfei Ren, Xin Dong, Xuanxin Ding, Jiaming Song, Jing Zhang, Taiwen Li, Chenfei Wang
Summary: Understanding gene expression patterns across different human cell types is crucial for investigating mechanisms of cell type differentiation and disease occurrence and progression. HUSCH is a large-scale database that integrates high-quality single-cell transcriptomic datasets from different tissues, providing comprehensive visualization and analysis of gene expression.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Microbiology
Elisabet Alacid, Thomas A. Richards
Summary: Natural environments consist of diverse microorganisms interacting to form functional networks. The application of single-cell technologies has revolutionized the understanding of development and disease. Methods such as cell atlases can now be combined with cellular imaging to quantify microbe interactions, transforming our understanding of ecological interactions.
CURRENT OPINION IN MICROBIOLOGY
(2021)
Review
Genetics & Heredity
Magda Mareckova, Hassan Massalha, Valentina Lorenzi, Roser Vento-Tormo
Summary: This article discusses the construction of cellular atlases of the human reproductive system using single-cell technologies and explores the significance of these maps in understanding reproductive pathologies and dissecting the heterogeneity of in vitro model systems.
ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS
(2022)
Article
Biochemical Research Methods
Valeria Garcia-Flores, Yi Xu, Errile Pusod, Roberto Romero, Roger Pique-Regi, Nardhy Gomez-Lopez
Summary: Single-cell RNA-sequencing (scRNA-seq) is a powerful tool to study cellular composition and interactions in complex tissues. This study presents a protocol for preparing high-quality single-cell suspensions from human placental tissues, including the basal plate, placental villi, and chorioamniotic membranes. The protocol includes tissue collection, tailored dissociation procedures, and cryopreservation of single-cell suspensions. The resulting suspensions are compatible with droplet-based scRNA-seq technology and exhibit high yield and viability. The entire process takes approximately 6 hours, with an additional 2 hours for thawing of cryopreserved single cells.
Article
Multidisciplinary Sciences
Philippe Jean, Fabienne Wong Jun Tai, Amrit Singh-Estivalet, Andrea Lelli, Cyril Scandola, Sebastien Megharba, Sandrine Schmutz, Solene Roux, Sabrina Mechaussier, Muriel Sudres, Enguerran Mouly, Anne-Valerie Heritier, Crystel Bonnet, Adeline Mallet, Sophie Novault, Valentina Libri, Christine Petit, Nicolas Michalski
Summary: Functional molecular characterization of the cochlea has mainly been driven by the deciphering of the genetic architecture of sensorineural deafness. By analyzing the single-cell transcriptomic atlas of the mouse cochlea, researchers have identified almost all cochlear cell types and discovered three cell types, providing insights into the gene regulatory networks controlling cochlear cell differentiation and maturation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Duo Chen, Mingwei Shao, Yi Song, Gaofei Ren, Feng Guo, Xunjie Fan, Yanyan Wang, Wei Zhang, Guijun Qin
Summary: Diabetic kidney disease (DKD), affecting 40% of diabetic patients, is the leading cause of chronic kidney disease worldwide. Through single-cell RNA sequencing and spatial transcriptomic analyses, distinct cell clusters, differentially expressed genes, and cell-cell interactions were identified in kidney specimens from DKD patients. Inflammatory signaling pathways were primarily enriched in most kidney parenchymal cells in DKD. Intercellular crosstalk primarily involved chemokines in DKD. Furthermore, spatial transcriptomics revealed the co-localization of venous endothelial cells and fibroblasts, with immune cells enriched in areas of renal fibrosis. These findings provide valuable insights into DKD pathogenesis and potential therapeutic targets.
Review
Cell Biology
Maria A. Dimitriu, Irina Lazar-Contes, Martin Roszkowski, Isabelle M. Mansuy
Summary: Recent advances in single-cell analyses have led to comprehensive characterization of cellular and molecular states, with the development of multiplexed assays offering simultaneous analysis of multiple factors and processes. These technologies have rapidly evolved, providing better specificity, precision, and resolution. This review summarizes recent progress in single-cell multiomics approaches, focusing on innovative techniques that integrate genome, epigenome, and transcriptome profiling.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Developmental Biology
Nicholas M. Negretti, Erin J. Plosa, John T. Benjamin, Bryce A. Schuler, A. Christian Habermann, Christopher S. Jetter, Peter Gulleman, Claire Bunn, Alice N. Hackett, Meaghan Ransom, Chase J. Taylor, David Nichols, Brittany K. Matlock, Susan H. Guttentag, Timothy S. Blackwell, Nicholas E. Banovich, Jonathan A. Kropski, Jennifer M. S. Sucre
Summary: This study used single-cell RNA sequencing to explore the dynamic alterations in parenchymal cells during lung organogenesis in mice. The research revealed lineage relationships of epithelial, endothelial, and mesenchymal cells at different developmental stages, providing a comprehensive view of cellular dynamics in lung organogenesis. The findings highlighted the complexity of type 1 pneumocyte function and characterized the expression patterns of mesenchymal Wnt during crucial stages of lung development.
Article
Multidisciplinary Sciences
Pierfrancesco Pagella, Laura de Vargas Roditi, Bernd Stadlinger, Andreas E. Moor, Thimios A. Mitsiadis
Summary: This study mapped the transcriptional landscape of various cell populations in human teeth at single-cell resolution, analyzing their stem cell populations and microenvironment in detail. The research revealed significant cellular heterogeneity in dental pulp and periodontium, with similar molecular signatures of stem cell populations but divergent microenvironments. The findings suggest that microenvironmental specificity could be a key factor in functional differences between highly similar stem cells, potentially influencing cell-based dental therapeutic approaches.
Review
Biochemistry & Molecular Biology
Yu-Sheng Wang, Jia Guo
Summary: The ability to quantify a large number of varied transcripts in single cells in their native spatial context is crucial for understanding health and disease, and recent advances in multiplexed FISH methods have enabled comprehensive RNA profiling in individual cells.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Multidisciplinary Sciences
LiangYu Zhao, Sha Han, HengChuan Su, JianYing Li, ErLei Zhi, Peng Li, ChenCheng Yao, RuHui Tian, HuiXing Chen, HuiRong Chen, JiaQiang Luo, ChenKun Shi, ZhiYong Ji, JianLin Hu, Gang Wu, WeiDong Zhou, YuXin Tang, YuZhuo Chen, GuiTing Lin, Tom F. Lue, DengLong Wu, Zheng Li
Summary: This study provides insights into the cellular heterogeneity and signalling networks of the human corpus cavernosum. It describes the spatial distribution of different cell types and identifies potential regulatory signalling pathways in erectile dysfunction.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Meng Zhang, Stephen W. Eichhorn, Brian Zingg, Zizhen Yao, Kaelan Cotter, Hongkui Zeng, Hongwei Dong, Xiaowei Zhuang
Summary: A single-cell transcriptome-imaging method, MERFISH, was used to create a molecularly defined and spatially resolved cell atlas of the mouse primary motor cortex. Approximately 300,000 cells were profiled, revealing 95 neuronal and non-neuronal cell clusters and a complex spatial map. Integration of MERFISH with retrograde labelling showed that cortical projections from neurons formed a complex network with individual clusters projecting to multiple target regions.
Review
Medicine, Research & Experimental
Nafiseh Erfanian, A. Ali Heydari, Adib Miraki Feriz, Pablo Ianez, Afshin Derakhshani, Mohammad Ghasemigol, Mohsen Farahpour, Seyyed Mohammad Razavi, Saeed Nasseri, Hossein Safarpour, Amirhossein Sahebkar
Summary: Traditional bulk sequencing methods have limitations in measuring cell groups, masking heterogeneity and rare populations. Single-cell resolution improves understanding of complex biological systems and diseases, but also generates high-dimensional, sparse, and complex data that makes analysis difficult. Deep learning has shown promising results in single-cell omics for data preprocessing and downstream analysis, but has not revolutionized the field yet. However, recent advances reveal its valuable resources in fast-tracking and advancing research in single-cell.
BIOMEDICINE & PHARMACOTHERAPY
(2023)
Article
Biotechnology & Applied Microbiology
Isar Nassiri, Benjamin Fairfax, Angela Lee, Yanxia Wu, David Buck, Paolo Piazza
Summary: This study presents an R package, scQCEA, for quality control and enrichment analysis of single-cell RNA sequencing data. It can generate reports and visualize quality scores for comparison and evaluation. It also provides automated cell type annotation and reference gene sets. The tool allows examination of biases and outliers and objective selection of optimal cluster numbers before downstream analysis. Rating: 8/10.
Review
Plant Sciences
Yajin Mo, Yuling Jiao
Summary: Single-cell sequencing approaches provide insights into the intracellular dynamics of individual cells and have vast applications in plant biology. This article introduces the current advances in single-cell omics, particularly in genome and transcriptome sequencing. Benchmarking studies are used to highlight the progress made in this field. The article also discusses future opportunities and challenges for the widespread adoption of single-cell sequencing techniques in plant biology.
Article
Biology
Alper Akay, David Jordan, Isabela Cunha Navarro, Tomasz Wrzesinski, Chris P. Ponting, Eric A. Miska, Wilfried Haerty
Article
Multidisciplinary Sciences
Harry Clifford, Anna Dulneva, Chris P. Ponting, Wilfried Haerty, Esther B. E. Becker
SCIENTIFIC REPORTS
(2019)
Article
Biochemistry & Molecular Biology
Kerstin Koehler, Luis Sanchez-Pulido, Verena Hoefer, Anika Marko, Chris P. Ponting, Ambrosius P. Snijders, Regina Feederle, Aloys Schepers, Dominik Boos
Article
Cardiac & Cardiovascular Systems
Ian R. McCracken, Richard S. Taylor, Fatma O. Kok, Fernando de la Cuesta, Ross Dobie, Beth E. P. Henderson, Joanne C. Mountford, Axelle Caudrillier, Neil C. Henderson, Chris P. Ponting, Andrew H. Baker
EUROPEAN HEART JOURNAL
(2020)
Article
Biochemical Research Methods
Luis Sanchez-Pulido, Chris P. Ponting
Article
Oncology
Jana Travnickova, Sonia Wojciechowska, Ava Khamseh, Philippe Gautier, Daniel V. Brown, Thomas Lefevre, Alessandro Brombin, Ailith Ewing, Amy Capper, Michaela Spitzer, Ramile Dilshat, Colin A. Semple, Marie E. Mathers, James A. Lister, Eirikur Steingrimsson, Thierry Voet, Chris P. Ponting, E. Elizabeth Patton
Article
Biochemistry & Molecular Biology
Fatima Dhalla, Jeanette Baran-Gale, Stefano Maio, Lia Chappell, Georg A. Hollaender, Chris P. Ponting
Article
Multidisciplinary Sciences
P. Ramachandran, R. Dobie, J. R. Wilson-Kanamori, E. F. Dora, B. E. P. Henderson, N. T. Luu, J. R. Portman, K. P. Matchett, M. Brice, J. A. Marwick, R. S. Taylor, M. Efremova, R. Vento-Tormo, N. O. Carragher, T. J. Kendall, J. A. Fallowfield, E. M. Harrison, D. J. Mole, S. J. Wigmore, P. N. Newsome, C. J. Weston, J. P. Iredale, F. Tacke, J. W. Pollard, C. P. Ponting, J. C. Marioni, S. A. Teichmann, N. C. Henderson
Article
Cell Biology
Ross Dobie, John R. Wilson-Kanamori, Beth E. P. Henderson, James R. Smith, Kylie P. Matchett, Jordan R. Portman, Karolina Wallenborg, Simone Picelli, Anna Zagorska, Swetha V. Pendem, Thomas E. Hudson, Minnie M. Wu, Grant R. Budas, David G. Breckenridge, Ewen M. Harrison, Damian J. Mole, Stephen J. Wigmore, Prakash Ramachandran, Chris P. Ponting, Sarah A. Teichmann, John C. Marioni, Neil C. Henderson
Article
Multidisciplinary Sciences
Mykhailo Y. Batiuk, Araks Martirosyan, Jerome Wahis, Filip de Vin, Catherine Marneffe, Carola Kusserow, Jordan Koeppen, Joao Filipe Viana, Joao Filipe Oliveira, Thierry Voet, Chris P. Ponting, T. Grant Belgard, Matthew G. Holt
NATURE COMMUNICATIONS
(2020)
Article
Genetics & Heredity
Andrew D. Bretherick, Oriol Canela-Xandri, Peter K. Joshi, David W. Clark, Konrad Rawlik, Thibaud S. Boutin, Yanni Zeng, Carmen Amador, Pau Navarro, Igor Rudan, Alan F. Wright, Harry Campbell, Veronique Vitart, Caroline Hayward, James F. Wilson, Albert Tenesa, Chris P. Ponting, J. Kenneth Baillie, Chris Haley
Article
Biochemistry & Molecular Biology
Thomas F. M. Cummings, Kevin Gori, Luis Sanchez-Pulido, Gavriil Gavriilidis, David Moi, Abigail R. Wilson, Elizabeth Murchison, Christophe Dessimoz, Chris P. Ponting, Maria A. Christophorou
Summary: Protein posttranslational modifications add complexity to biological systems. This study reveals the evolutionary trajectory of peptidylarginine deiminases (PADIs) in animals and provides evidence that PADIs were introduced into animals through horizontal gene transfer from cyanobacteria.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biology
Pedro Ferreira, Luis Sanchez-Pulido, Anika Marko, Chris P. Ponting, Dominik Boos
Summary: The faithful duplication of the genome requires controlled replication origin firing. The proteins Treslin/TICRR and its yeast counterpart Sld3 play a crucial role in regulating the firing of replication origins. A revised domain architecture model of Treslin/TICRR is proposed, revealing a conserved beta-barrel fold in the middle domain (M domain) shared by Treslin/TICRR and Sld3. It is found that Treslin/Sld3 and MTBP/Sld7 engage in homotypic interactions similar to the dimerization of Ku70-Ku80. Mutants of the Treslin/TICRR domain indicate the importance of all Sld3-core domains and the non-conserved terminal domains during origin firing in human cells.
LIFE SCIENCE ALLIANCE
(2022)
Article
Cardiac & Cardiovascular Systems
Ian R. McCracken, Ross Dobie, Matthew Bennett, Rainha Passi, Abdelaziz Beqqali, Neil C. Henderson, Joanne C. Mountford, Paul R. Riley, Chris P. Ponting, Nicola Smart, Mairi Brittan, Andrew H. Baker
Summary: The study aims to characterize the transcriptome of human foetal cardiac endothelium using single-cell RNA sequencing (scRNA-seq) to provide insights into cellular heterogeneity and transcriptional dynamics underlying endothelial specification. Results reveal distinct endothelial cell populations, endocardial contribution to coronary vasculature, and arterial specification of capillary endothelium. Transcriptional signatures defining endothelial subpopulations are largely conserved between human and mouse, with MECOM playing a role in maintaining arterial endothelial identity.
CARDIOVASCULAR RESEARCH
(2022)