Review
Genetics & Heredity
Waleed Iqbal, Wanding Zhou
Summary: Understanding tissue heterogeneity requires analyzing intercellular epigenetic differences at the single-cell level. Recent advances in single-cell DNA methylome profiling have provided the tools to study this heterogeneity in detail. However, these advances also bring challenges in data analysis and interpretation.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Mariia Bilous, Loc Tran, Chiara Cianciaruso, Aurelie Gabriel, Hugo Michel, Santiago J. Carmona, Mikael J. Pittet, David Gfeller
Summary: SuperCell is a framework that efficiently combines highly similar cells into metacells, preserving and accelerating the results of single-cell RNA sequencing data analysis.
BMC BIOINFORMATICS
(2022)
Article
Immunology
Qikai Tang, Zhengxin Chen, Jiaheng Xie, Chuangqi Mo, Jiacheng Lu, Qixiang Zhang, Zhangjie Wang, Wei Wu, Huibo Wang
Summary: This study investigates the role of ubiquitination genes in gliomas and identifies USP4 as a potential biomarker for glioma. The findings suggest that this research provides new insights for the treatment and immunotherapy of glioma.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Cell Biology
Yi-Rong Jiang, Le Zhu, Lan-Rui Cao, Qiong Wu, Jian-Bo Chen, Yu Wang, Jie Wu, Tian-Yu Zhang, Zhao-Lun Wang, Zhi-Ying Guan, Qin-Qin Xu, Qian-Xi Fan, Shao-Wen Shi, Hui-Feng Wang, Jian-Zhan Pan, Xu-Dong Fu, Yongcheng Wang, Qun Fang
Summary: A new single-cell analysis platform, capable of simultaneously analyzing the transcriptome and proteome, provides an important resource for understanding the relationship between transcription and translation in cells. By applying this platform to mouse oocytes, we investigated the correlation between RNA and protein, as well as the meiosis regulatory network, and identified specific oocyte maturational signatures.
Article
Biochemistry & Molecular Biology
Ya Han, Yuting Wang, Xin Dong, Dongqing Sun, Zhaoyang Liu, Jiali Yue, Haiyun Wang, Taiwen Li, Chenfei Wang
Summary: TISCH2 is a resource of single-cell RNA-seq data from tumors, providing comprehensive analysis of gene expression in the tumor microenvironment. With added features, users can better utilize the large-scale datasets for analysis and visualization.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Immunology
Maria L. Elkjaer, Richard Roettger, Jan Baumbach, Zsolt Illes
Summary: Multiple sclerosis is an inflammatory disease of the central nervous system, and there is still a lack of understanding about its pathological process and predictive biomarkers for disease progression. Novel viewpoints in systems biology offer a better understanding of key pathological pathways, but there are still unanswered questions. Research has discovered several molecules and networks that may contribute to the pathogenesis of multiple sclerosis.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Genetics & Heredity
Ernesto Paas-Oliveros, Enrique Hernandez-Lemus, Guillermo de Anda-Jauregui
Summary: This paper provides a comprehensive overview of the significance and applications of single cell computational analysis in oncology. It discusses key computational techniques and challenges, including data quality control, normalization, clustering, and future directions such as machine learning and deep learning approaches.
FRONTIERS IN GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Jin-Mi Oh, Minae An, Dae-Soon Son, Jinhyuk Choi, Yong Beom Cho, Chang Eun Yoo, Woong-Yang Park
Summary: There are differences in the proportions of cell types between single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA sequencing (snRNA-seq). The proportion of immune cells is relatively high in scRNA-seq, while the proportion of epithelial cells in the colon and hepatocytes in the liver is relatively high in snRNA-seq.
EXPERIMENTAL AND MOLECULAR MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Ruowen Zhao, Wenhao Han, Kailin Tang, Ruru Shao, Pingyi Zhu, Shi Zhang, Pan Xu, Yuan He
Summary: This study used single-cell transcriptome sequencing to map the normal oral mucosal cells and identified different cell groups and their interactions, providing basic data resources for further research on oral mucosal diseases.
JOURNAL OF CELLULAR BIOCHEMISTRY
(2022)
Article
Biology
Yunhe Liu, Aoshen Wu, Xueqing Peng, Xiaona Liu, Gang Liu, Lei Liu
Summary: The developed scRNA simulation algorithm is able to recreate the actual data generation process, discover the impact of parameters on classification, compare normalization and clustering algorithms, and provide new insights into scRNA analysis.
Article
Biology
Shudong Wang, Yu Zhang, Yulin Zhang, Wenhao Wu, Lan Ye, Yunyin Li, Jionglong Su, Shanchen Pang
Summary: Single-cell RNA sequencing (scRNA-seq) is a successful technique for identifying cellular heterogeneity. In this study, an unsupervised clustering method called scASGC is proposed, which outperforms classical and state-of-the-art methods, and is able to accurately identify cell subpopulations.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Immunology
Liang Chen, Xueming Zhang, Qixiang Zhang, Tao Zhang, Jiaheng Xie, Wei Wei, Ying Wang, Hongzhu Yu, Hongkun Zhou
Summary: In this study, we constructed a necroptosis-related signature in pancreatic cancer using transcriptome and single-cell sequencing analysis. Patients with high levels of this signature showed significantly poorer prognosis, along with significant differences in immune infiltration and mutation levels compared to patients with low levels of the signature.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Immunology
Tomi Suomi, Laura L. Elo
Summary: Mass spectrometry proteomics is essential in modern immunology, providing insights into protein expression, localization, modifications, and interactions of immune cells. Computational approaches have advanced the analysis of large protein profiling datasets and allowed for further exploration of the immune system. Recent studies have focused on human CD4+ T cells and their subtypes, giving valuable information on their proteome.
IMMUNOLOGY LETTERS
(2022)
Review
Biochemistry & Molecular Biology
Rahul Shaw, Xin Tian, Jian Xu
Summary: The adoption of single-cell RNA sequencing technology has revolutionized the transcriptome analysis, allowing for better understanding of tissue and cellular heterogeneity and rapid identification of rare cell types. In the field of plant sciences, single-cell transcriptome profiling is in its early stages and presents exciting challenges to overcome.
Editorial Material
Multidisciplinary Sciences
Jeffrey A. Farrell
Summary: CellOracle, a computational tool, can predict the interaction of gene networks in programming cell identity during embryonic development. This tool will contribute to a better understanding of the regulation of development.
Article
Cell Biology
Laetitia Dubouchet, Helena Todorov, Ruth Seurinck, Nicolas Vallet, Sofie Van Gassen, Aurelien Corneau, Catherine Blanc, Habib Zouali, Anne Boland, Jean-Francois Deleuze, Brian Ingram, Regis Peffault de Latour, Yvan Saeys, Gerard Socie, David Michonneau
Summary: This study reveals the mechanisms underlying operational tolerance after hematopoietic stem cell transplantation in humans. It shows that primary tolerance is associated with long-lasting reshaping of the immune system, involving an increase in regulatory T cell subsets and a decrease in T cell activation, proliferation, and migration. The study also identifies the role of nicotinamide adenine dinucleotide biosynthesis in immune cell function regulation and suggests a balance between a CD38-activated immune state and CD73-related production of adenosine as a key regulator of operational tolerance.
SCIENCE TRANSLATIONAL MEDICINE
(2022)
Review
Genetics & Heredity
Artuur Couckuyt, Ruth Seurinck, Annelies Emmaneel, Katrien Quintelier, David Novak, Sofie Van Gassen, Yvan Saeys
Summary: Translational machine learning refers to the collaborative efforts between data scientists and clinicians in applying machine learning algorithms to clinical decision support systems. This collaboration improves interpretability and trust, aiming to produce generalizable and reproducible models. Collaboration and data sharing are highly recommended to tackle the challenges involved in translational machine learning.
Article
Multidisciplinary Sciences
Samya Van Coillie, Emily Van San, Ines Goetschalckx, Bartosz Wiernicki, Banibrata Mukhopadhyay, Wulf Tonnus, Sze Men Choi, Ria Roelandt, Catalina Dumitrascu, Ludwig Lamberts, Geert Dams, Wannes Weyts, Jelle Huysentruyt, Behrouz Hassannia, Irina Ingold, Suhas Lele, Evelyne Meyer, Maya Berg, Ruth Seurinck, Yvan Saeys, An Vermeulen, Alexander L. N. van Nuijs, Marcus Conrad, Andreas Linkermann, Mohan Rajapurkar, Peter Vandenabeele, Eric Hoste, Koen Augustyns, Tom Vanden Berghe
Summary: The development of multiorgan dysfunction syndrome (MODS) is the most common cause of death in the intensive care unit (ICU). Catalytic iron is associated with ICU mortality and may induce excessive lipid peroxidation, leading to cellular toxicity and multiorgan dysfunction. Blocking lipid peroxidation with a ferrostatin-analogue can protect mice from injury and death in experimental non-septic MODS.
NATURE COMMUNICATIONS
(2022)
Meeting Abstract
Rheumatology
P. Rybakowska, S. van Gassen, C. Perez-Sanchez, A. Ibanez-Costa, N. Varela, R. Ortega Castro, C. Fernandez-Roldan, I. Jimenez-Moleon, N. Ortego, E. Raya, R. Aguilar Quesada, C. Lopez-Pedrera, E. Collantes Estevez, Y. Saeys, M. Alarcon-Riquelme, C. Maranon
ANNALS OF THE RHEUMATIC DISEASES
(2022)
Article
Oncology
Nele Loret, Niels Vandamme, Jordy De Coninck, Joachim Taminau, Kato De Clercq, Gillian Blancke, Sven Jonckheere, Steven Goossens, Kelly Lemeire, Sofie De Prijck, Kevin Verstaen, Ruth Seurinck, Jo Van Dorpe, Steven Weyers, Hannelore Denys, Koen van de Vijver, Bart N. Lambrecht, Philippe Tummers, Yvan Saeys, Geert Berx
Summary: This study used single-cell RNA sequencing to analyze cells from HGSOC patients, revealing the concordance between lesions and the differences in transcriptional profiles between ascitic and solid cancer cells. Additionally, different subtypes of cancer-associated fibroblasts were identified. These findings suggest that tumor and stromal cell heterogeneity plays a crucial role in therapy resistance in HGSOC and may inform novel therapeutic strategies.
MOLECULAR CANCER RESEARCH
(2022)
Article
Biochemical Research Methods
Isabelle Scheyltjens, Hannah Van Hove, Karen De Vlaminck, Daliya Kancheva, Jonathan Bastos, Monica Vara-Perez, Ana Rita Pombo Antunes, Liesbet Martens, Charlotte L. Scott, Jo A. Van Ginderachter, Yvan Saeys, Martin Guilliams, Niels Vandamme, Kiavash Movahedi
Summary: This protocol provides a detailed workflow for single-cell multi-omic analysis of the mouse brain immune compartment. It includes steps for brain dissection, cell dissociation, high-dimensional flow cytometry, droplet-based single-cell RNA sequencing, and analysis of the data. This optimized workflow allows for a comprehensive assessment of immune cell heterogeneity and activation in the brain, which is crucial for studying neurological disorders.
Article
Multidisciplinary Sciences
Helena Todorov, Margaux Prieux, Daphne Laubreton, Matteo Bouvier, Shaoying Wang, Simon de Bernard, Christophe Arpin, Robrecht Cannoodt, Wouter Saelens, Arnaud Bonnaffoux, Olivier Gandrillon, Fabien Crauste, Yvan Saeys, Jacqueline Marvel
Summary: In this study, the generation of memory precursor cells following acute infection was investigated using single-cell RNA-seq data. The researchers found that these memory precursors are continuously generated, with the number increasing over time. Additionally, the expression of genes associated with effector functions was also found to increase in memory precursors at later time points.
Article
Biochemistry & Molecular Biology
Dena Panovska, Pouya Nazari, Basiel Cole, Pieter-Jan Creemers, Marleen Derweduwe, Lien Solie, Sofie Van Gassen, Annelies Claeys, Tatjana Verbeke, Elizabeth F. Cohen, Michael Y. Tolstorukov, Yvan Saeys, David van der Planken, Francesca M. Bosisio, Eric Put, Sven Bamps, Paul M. Clement, Michiel Verfaillie, Raf Sciot, Keith L. Ligon, Steven De Vleeschouwer, Asier Antoranz, Frederik De Smet
Summary: The PROSPERO assay is a precise method to evaluate therapy efficacy by measuring molecular drug responses in freshly resected brain tumor samples. It provides key functional insights in cellular behavior and can complement standard clinical biomarker evaluations.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2023)
Letter
Oncology
Margot F. van Spronsen, Sophie Horrevorts, Claudia Cali, Theresia M. Westers, Sofie Van Gassen, Yvan Saeys, Sandra J. van Vliet, Yvette van Kooyk, Arjan A. van de Loosdrecht
Article
Rheumatology
Celine Mortier, Katrien Quintelier, Ann-Sophie De Craemer, Thomas Renson, Liselotte Deroo, Emilie Dumas, Eveline Verheugen, Julie Coudenys, Tine Decruy, Zuzanna Lukasik, Sofie Van Gassen, Yvan Saeys, Anne Hoorens, Triana Lobaton, Filip van den Bosch, Tom van de Wiele, Koen Venken, Dirk Elewaut
Summary: The study found marked type 17 skewing in the inflamed gut mucosa of patients with nonradiographic axial SpA, linked to gamma delta-hi T cells and associated with intestinal inflammation and disease activity.
ARTHRITIS & RHEUMATOLOGY
(2023)
Article
Microbiology
Helena Todorov, Tania Miguel Trabajo, Jan Roelof van der Meer
Summary: Bacterial growth at the single cell level can be studied using time-lapse microscopy imaging. This paper presents STrack, a tool that tracks cells in time-lapse images in a fast and efficient way. Compared to other tracking tools, STrack shows higher consistency, returning over 80% correct cell lineages on average.
Review
Biochemistry & Molecular Biology
Corinne Urwyler-Rosselet, Giel Tanghe, Michael Devos, Paco Hulpiau, Yvan Saeys, Wim Declercq
Summary: Receptor interacting protein kinases (RIPKs) are a family of enzymes that play important roles in integrating stress signals in the skin homeostasis. By activating various signaling pathways, RIPKs regulate the activation of NF-& kappa;B and mitogen-activated protein kinases, influencing processes such as cell death, inflammation, differentiation, and Wnt signaling.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2023)
Letter
Biotechnology & Applied Microbiology
Anthony Sonrel, Almut Luetge, Charlotte Soneson, Izaskun Mallona, Pierre-Luc Germain, Sergey Knyazev, Jeroen Gilis, Reto Gerber, Ruth Seurinck, Dominique Paul, Emanuel Sonder, Helena L. L. Crowell, Imran Fanaswala, Ahmad Al-Ajami, Elyas Heidari, Stephan Schmeing, Stefan Milosavljevic, Yvan Saeys, Serghei Mangul, Mark D. Robinson
Summary: Computational methods are crucial in modern molecular biology. Benchmarking is critical in dissecting analysis pipelines, evaluating performance, and guiding users on tool selection. It also plays a key role in community building and advancing methods.
Article
Biochemical Research Methods
Paulina Rybakowska, Sofie Van Gassen, Jordi Martorell Marugan, Katrien Quintelier, Yvan Saeys, Marta E. Alarcon-Riquelme, Concepcion Maranon
Summary: In this article, a protocol for whole blood analysis in mass cytometry (MC) is presented, along with an R package called Cyto Quality Pipeline (CytoQP), which aims to minimize experimental artifacts and batch effects for data reproducibility. The article outlines the steps for stimulating, fixing, and freezing blood samples prior to acquisition, making them suitable for retrospective studies. The use of bar-coding and reference samples for multicenter and multi-batch experiments is also described.
