Article
Multidisciplinary Sciences
Richard C. Tyser, Elmir Mahammadov, Shota Nakanoh, Ludovic Vallier, Antonio Scialdone, Shankar Srinivas
Summary: The single-cell transcriptional profile of a human embryo between 16 and 19 days after fertilization shows similarities and differences in gastrulation compared to mouse and non-human primate models. This study provides new insights into human development and offers valuable information for directed differentiation of human cells in vitro.
Article
Multidisciplinary Sciences
Kai Battenberg, S. Thomas Kelly, Radu Abu Ras, Nicola A. Hetherington, Makoto Hayashi, Aki Minoda
Summary: Single-cell RNA-sequencing analysis has gained popularity, and UniverSC is a universal tool for processing single-cell RNA-seq data on any platform. It provides a command-line tool, docker image, and containerized graphical application for consistent and comprehensive integration, comparison, and evaluation of data from various platforms. Additionally, a cross-platform application with a graphical user interface is available to address the bottleneck of data processing for researchers without bioinformatics expertise.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Malte D. Luecken, M. Buettner, K. Chaichoompu, A. Danese, M. Interlandi, M. F. Mueller, D. C. Strobl, L. Zappia, M. Dugas, M. Colome-Tatche, Fabian J. Theis
Summary: This study benchmarked 68 method and preprocessing combinations on 85 batches of gene expression data, highlighting the importance of highly variable gene selection in improving method performance. When dealing with complex integration tasks, scANVI, Scanorama, scVI, and scGen consistently performed well, while the performance of single-cell ATAC-sequencing integration was strongly influenced by the choice of feature space.
Article
Nutrition & Dietetics
Qianwen Han, Haiyan Li, Fen Zhao, Ji'an Gao, Xinqi Liu, Biao Ma
Summary: This study investigated the anti-aging effects and mechanism of Auricularia auricula peptides (AAPs) on HepG2 cells. The results showed that AAPs could reduce intracellular reactive oxygen species (ROS) and malondialdehyde (MDA) levels, increase antioxidant enzyme activities, and inhibit senescence. Furthermore, AAPs could also inhibit inflammation through the MAPK/NF-κB signaling pathway, delaying cell senescence.
Article
Biochemistry & Molecular Biology
Jacob C. Kimmel, David R. Kelley
Summary: scNym is a semi-supervised adversarial neural network that can transfer cell identity annotations between different experiments by learning rich representations of cell identities from both labeled and unlabeled datasets. It shows superior performance in transferring annotations across experiments and can synthesize information from multiple datasets to improve accuracy. Additionally, scNym models are well calibrated, interpretable, and can be enhanced with saliency methods.
Article
Biochemistry & Molecular Biology
Mengwei Li, Xiaomeng Zhang, Kok Siong Ang, Jingjing Ling, Raman Sethi, Nicole Yee Shin Lee, Florent Ginhoux, Jinmiao Chen
Summary: DISCO is an integrated database of single-cell omics data, offering an integrated cell atlas and harmonized metadata that users can utilize for comprehensive single-cell data analysis and exploration.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Dakota Y. Hawkins, Daniel T. Zuch, James Huth, Nahomie Rodriguez-Sastre, Kelley R. McCutcheon, Abigail Glick, Alexandra T. Lion, Christopher F. Thomas, Abigail E. Descoteaux, William Evan Johnson, Cynthia A. Bradham
Summary: In this study, a novel unsupervised algorithm called ICAT is proposed, which can accurately identify and resolve cell states in single-cell RNA sequencing experiments, especially in perturbation experiments, where cell states need to be matched and population substructure needs to be removed. Through validation using simulated and real datasets, it is shown that ICAT outperforms current integration workflows and is robust to various conditions. Empirical validation in a developmental model demonstrates that only ICAT can identify perturbation-unique cellular responses.
Article
Biochemical Research Methods
Qianqian Zhang, Xing Xu, Li Lin, Jian Yang, Xing Na, Xin Chen, Lingling Wu, Jia Song, Chaoyong Yang
Summary: Cilo-seq is a high-performance platform for single-cell RNA sequencing library construction. It utilizes digital microfluidics in a single device, enabling convenient single-cell isolation, efficient nucleic acid amplification, low-loss nucleic acid purification, and high-quality library preparation.
Article
Multidisciplinary Sciences
Lieke Michielsen, Marcel J. T. Reinders, Ahmed Mahfouz
Summary: scHPL is a hierarchical progressive learning method that can learn cellular hierarchies from multiple datasets while preserving the original annotations.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Alexander Gerniers, Orian Bricard, Pierre Dupont
Summary: This study presents a data mining method, MicroCellClust, to identify small subpopulations of cells with highly specific expression profiles. Through controlled experiments, it is shown to achieve a high F-1 score in identifying rare subpopulations of human T cells, specific CD4 T cells from breast cancer samples, and a subpopulation related to a specific stage in the cell cycle. Additionally, three rare subpopulations in mouse embryonic stem cells are successfully identified with MicroCellClust, demonstrating its effectiveness in identifying small subsets of cells with highly specific expression profiles.
Article
Biology
Thomas L. Williams, Maria T. Colzani, Robyn G. C. Macrae, Emma L. Robinson, Stuart Bloor, Edward J. D. Greenwood, Jun Ru Zhan, Gregory Strachan, Rhoda E. Kuc, Duuamene Nyimanu, Janet J. Maguire, Paul J. Lehner, Sanjay Sinha, Anthony P. Davenport
Summary: Patients with cardiovascular comorbidities are more vulnerable to severe infection with SARS-CoV-2, which can directly harm cardiovascular tissue. Researchers have developed a screening platform using human embryonic stem cell-derived cardiomyocytes to identify new inhibitors of SARS-CoV-2 infection, with benztropine and DX600 found as potential inhibitors. This discovery of new medicines is crucial for protecting the heart in SARS-CoV-2 patients and those who cannot be vaccinated.
COMMUNICATIONS BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Joachim De Jonghe, Tomasz S. Kaminski, David B. Morse, Marcin Tabaka, Anna L. Ellermann, Timo N. Kohler, Gianluca Amadei, Charlotte E. Handford, Gregory M. Findlay, Magdalena Zernicka-Goetz, Sarah A. Teichmann, Florian Hollfelder
Summary: The authors developed spinDrop, a technique that increases gene detection and reduces noise in droplet microfluidics, to generate a high-quality molecular atlas of mouse brain development.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Jordan W. Squair, Michael A. Skinnider, Matthieu Gautier, Leonard J. Foster, Gregoire Courtine
Summary: This study introduces a method called Augur for prioritizing the cell types most responsive to an experimental perturbation in complex tissue. By analyzing single-cell RNA-seq data, a list of cell types ranked based on separability following perturbation can be obtained. The study also demonstrates the application of this method in various workflows, including experimental designs, prioritization, and single-cell transcriptome imaging data.
Article
Biochemistry & Molecular Biology
Xin Shao, Haihong Yang, Xiang Zhuang, Jie Liao, Penghui Yang, Junyun Cheng, Xiaoyan Lu, Huajun Chen, Xiaohui Fan
Summary: scDeepSort is a pre-trained tool for cell-type annotation in single-cell transcriptomics using deep learning and a weighted graph neural network. It demonstrates high performance and robustness across multiple datasets, achieving an accuracy of 83.79%.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
Mohit Goyal, Guillermo Serrano, Josepmaria Argemi, Ilan Shomorony, Mikel Hernaez, Idoia Ochoa
Summary: The article introduces a neural-network-based framework JIND for automated cell-type identification. JIND performs integration in a suitably chosen space and employs a novel asymmetric alignment to address batch effects. Results demonstrate that the joint approach of integration and classification in JIND outperforms existing pipelines in accuracy and can identify cells that cannot be reliably classified.
Article
Biochemistry & Molecular Biology
Andrew M. Jobbins, Nejc Haberman, Natalia Artigas, Christopher Amourda, Helen A. B. Paterson, Sijia Yu, Samuel J. Blackford, Alex Montoya, Marian Dore, Yi-Fang Wang, Alessandro Sardini, Ines Cebola, Johannes Zuber, Sheikh Tamir Rashid, Boris Lenhard, Santiago Vernia
Summary: Pre-mRNA processing is altered in non-alcoholic fatty liver disease (NAFLD), with dysregulated alternative splicing and alternative polyadenylation. Decreased expression of SRSF10, a splicing factor, is associated with dysregulation of pre-mRNA processing in NAFLD.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Max J. Kellner, James J. Ross, Jakob Schnabl, Marcus P. S. Dekens, Martin Matl, Robert Heinen, Irina Grishkovskaya, Benedikt Bauer, Johannes Stadlmann, Luis Menendez-Arias, Andrew D. Straw, Robert Fritsche-Polanz, Marianna Traugott, Tamara Seitz, Alexander Zoufaly, Manuela Foedinger, Christoph Wenisch, Johannes Zuber, Andrea Pauli, Julius Brennecke
Summary: This article presents a rapid, robust, and sensitive RT-LAMP-based SARS-CoV-2 detection assay that bypasses the RNA isolation step and uses a colorimetric readout. The assay has been optimized and additional steps have been added to increase sensitivity and scalability. Open-source RT-LAMP enzymes and a version for home testing have also been developed.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Cell Biology
Clotilde Raynard, Xingjie Ma, Anda Huna, Nolwenn Tessier, Amelie Massemin, Kexin Zhu, Jean-Michel Flaman, Florentin Moulin, Delphine Goehrig, Jean-Jacques Medard, David Vindrieux, Isabelle Treilleux, Hector Hernandez-Vargas, Sylvie Ducreux, Nadine Martin, David Bernard
Summary: Cellular senescence is characterized by stable proliferation arrest and the acquisition of a senescence-associated secretory phenotype (SASP). The SASP affects the environment of senescent cells and can induce different phenotypic changes. This study reveals that the SASP can promote the neuroendocrine transdifferentiation (NED) of some epithelial cancer cells, providing insights into the functional link between senescent cell accumulation, NED, and clinical patient outcome.
Article
Hematology
Barbara Peter, Gregor Eisenwort, Irina Sadovnik, Karin Bauer, Michael Willmann, Thomas Ruelicke, Daniela Berger, Gabriele Stefanzl, Georg Greiner, Gregor Hoermann, Alexandra Keller, Dominik Wolf, Martin Culen, Georg E. Winter, Thomas Hoffmann, Ana-Iris Schiefer, Wolfgang R. Sperr, Johannes Zuber, Jiri Mayer, Peter Valent
Summary: In this study, targeting BRD4 and MYC was found to sensitize CML cells against BCR::ABL1 TKI, overcoming multiple forms of drug resistance in CML LSC.
AMERICAN JOURNAL OF HEMATOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Clotilde Raynard, Nolwenn Tessier, Anda Huna, Marine Warnier, Jean-Michel Flaman, Fabien Van Coppenolle, Sylvie Ducreux, Nadine Martin, David Bernard
Summary: The regulation of calcium ion (Ca2+) levels during cellular senescence is not well understood. This study found that several senescence inducers increased intracellular Ca2+ content in human mammary epithelial cells (HMECs), and the expression of the Ca2+-binding protein CALB1 was upregulated through the Ca2+-dependent calcineurin/NFAT pathway. Overexpression of CALB1 buffered the rise in intracellular Ca2+ levels observed in senescent cells. Additionally, increased expression of Ca2+-binding proteins calbindins was found to be a common marker of senescent cells. These findings suggest that Ca2+ and Ca2+-binding proteins play a crucial role in regulating cellular senescence.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Catarina Pechincha, Sven Groessl, Robert Kalis, Melanie de Almeida, Andrea Zanotti, Marten Wittmann, Martin Schneider, Rafael P. de Campos, Sarah Rieser, Marlene Brandstetter, Alexander Schleiffer, Karin Mueller-Decker, Dominic Helm, Sabrina Jabs, David Haselbach, Marius K. Lemberg, Johannes Zuber, Wilhelm Palm
Summary: Mammalian cells can generate amino acids through macropinocytosis and lysosomal breakdown of extracellular proteins, which cancer cells exploit for growth in nutrient-poor tumors. In this study, a transmembrane protein called LYSET was found to be selectively required for the consumption of extracellular proteins. LYSET is associated with GlcNAc-1-phosphotransferase in the Golgi, which targets catabolic enzymes to lysosomes. LYSET deficiency leads to a depletion of lysosomal enzymes and impairs the turnover of macropinocytic and autophagic cargoes.
Article
Immunology
Theresa Pinter, Maria Fischer, Markus Schaefer, Michaela Fellner, Julian Jude, Johannes Zuber, Meinrad Busslinger, Miriam Woehner
Summary: Plasma cells and plasmablasts are crucial for immune protection, and this study identified several new genes that are essential for plasmablast development through CRISPR-Cas9 screening.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Genetics & Heredity
Stefan Butz, Nina Schmolka, Ino D. Karemaker, Rodrigo Villasenor, Isabel Schwarz, Silvia Domcke, Esther C. H. Uijttewaal, Julian Jude, Florian Lienert, Arnaud R. Krebs, Nathalie P. de Wagenaar, Xue Bao, Johannes Zuber, Ulrich Elling, Dirk Schuebeler, Tuncay Baubec
Summary: Genomic imprinting is regulated by DNA methylation of imprinting control regions (ICRs) with parental-specificity. The epigenetic states of ICRs, despite having an identical DNA sequence, are determined by genetic and epigenetic factors. Through iterative integration of ICRs and DNA sequences, this study identified the DNA sequence features required for maintaining the epigenetic states in embryonic stem cells. Additionally, ATF7IP and ZMYM2 were found to be important for the stability of DNA and H3K9 methylation at ICRs in embryonic stem cells.
Article
Hematology
Marguerite-Marie Le Pannerer, Jeannine Diesch, Raquel Casquero, Michael Maher, Olga Garcia, Torsten Haferlach, Johannes Zuber, Andrea Kuendgen, Katharina S. Goetze, Marcus Buschbeck
Summary: This study identified several genes associated with the response to azacitidine (AZA) treatment in patients with myelodysplastic syndromes (MDS). These genes can be used to predict treatment response and the duration of treatment effectiveness. The genes identified are nonoverlapping, suggesting the need to develop combinatorial drug targets and response-predicting biomarkers for different gene sets.
Review
Cell Biology
Nadine Martin, Kexin Zhu, Joanna Czarnecka-Herok, Mathieu Vernier, David Bernard
Summary: Cellular senescence is a state of cell proliferation arrest accompanied by a specific secretory program, which affects the microenvironment of senescent cells. Various stresses can induce cellular senescence, such as telomere shortening, oncogene activation, oxidative or genotoxic stress. Cellular senescence plays a crucial role throughout life, showing beneficial effects in embryonic development and wound healing, but also detrimental effects in aging and aging-related diseases. In recent years, calcium and calcium signaling have been identified as critical factors in the implementation and regulation of cellular senescence. This review highlights the main discoveries in this field, including the increased intracellular calcium concentration in senescent cells, the identification of calcium-binding proteins, calcium channels (TRP, ITPR, ...), and MERCs (mitochondria-endoplasmic reticulum contact sites) as key players in this context.
Review
Cell Biology
Nadine Martin, Nikolay Popgeorgiev, Gabriel Ichim, David Bernard
Summary: In this Comment, the authors highlight the non-apoptotic roles of BCL-2 proteins in regulating cellular senescence and caution against the use of BCL-2 inhibitors as senolytics. While BCL-2 and related proteins are known for their role in apoptosis regulation, recent findings suggest their involvement in cellular senescence through non-apoptotic mechanisms.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2023)
Article
Biology
Changyu Zhu, Yadira M. Soto-Feliciano, John P. Morris, Chun-Hao Huang, Richard P. Koche, Yu-jui Ho, Ana Banito, Chun-Wei Chen, Aditya Shroff, Sha Tian, Geulah Livshits, Chi-Chao Chen, Myles Fennell, Scott A. Armstrong, C. David Allis, Darjus F. Tschaharganeh, Scott W. Lowe
Summary: Mutations in genes involved in chromatin modification and remodeling are frequently observed in human cancers. This study shows that MLL3 co-activates the Cdkn2a tumor suppressor gene by linking chromatin remodeling to tumor suppression. Disruption of Kmt2c and Myc overexpression cooperate to promote hepatocellular carcinoma development in mice.
Article
Cell Biology
Ana Guerrero, Andrew J. Innes, Pierre-Francois Roux, Sonja C. Buisman, Johannes Jung, Laura Ortet, Victoria Moiseeva, Verena Wagner, Lucas Robinson, Albertina Ausema, Anna Potapova, Eusebio Perdiguero, Ellen Weersing, Marieke Aarts, Nadine Martin, Torsten Wuestefeld, Pura Munoz-Canoves, Gerald de Haan, Oliver Bischof, Jesus Gil
Summary: 3-Deazaadenosine (3DA) is a promising drug that enhances the efficiency of cellular therapies by restraining senescence.
Article
Oncology
Birgit Wilding, Dirk Scharn, Dietrich Boese, Anke Baum, Valeria Santoro, Paolo Chetta, Renate Schnitzer, Dana A. Botesteanu, Christoph Reiser, Stefan Kornigg, Petr Knesl, Alexandra Hoermann, Anna Koeferle, Maja Corcokovic, Simone Lieb, Guido Scholz, Jens Bruchhaus, Markus Spina, Josef Balla, Biljana Peric-Simov, Jasmin Zimmer, Sophie Mitzner, Thomas N. Fett, Alexandra Beran, Lyne Lamarre, Thomas Gerstberger, Daniel Gerlach, Markus Bauer, Andreas Bergner, Andreas Schlattl, Gerd Bader, Matthias Treu, Harald Engelhardt, Stephan Zahn, Julian E. Fuchs, Johannes Zuber, Peter Ettmayer, Mark Pearson, Mark Petronczki, Norbert Kraut, Darryl B. McConnell, Flavio Solca, Ralph A. Neumuller
Summary: The study identifies potent inhibitors that selectively target HER2 exon 20 insertion mutations, providing a potential treatment option for non-small cell lung cancer.
Meeting Abstract
Pediatrics
S. Troester, J. Schmoellerl, T. Eder, G. Manhart, G. Winter, J. Zuber, F. Grebien
KLINISCHE PADIATRIE
(2022)