Review
Immunology
Kazuko Miyazaki, Masaki Miyazaki
Summary: This article discusses the driving factors of cell type-specific gene expression, emphasizing the importance of the interplay between chromatin architectures and TFs in cell fate decisions and cell type-specific functions, as well as the key roles of SEs and Rag1/2 genes in adaptive immunity.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Multidisciplinary Sciences
Reuben Franklin, Yiming Guo, Shiyang He, Meijuan Chen, Fei Ji, Xinyue Zhou, David Frankhouser, Brian T. Do, Carmen Chiem, Mihyun Jang, M. Andres Blanco, Matthew G. Vander Heiden, Russell C. Rockne, Maria Ninova, David B. Sykes, Konrad Hochedlinger, Rui Lu, Ruslan I. Sadreyev, Jernej Murn, Andrew Volk, Sihem Cheloufi
Summary: In this study, the authors demonstrate that CAF-1 maintains lineage fidelity by controlling chromatin accessibility at specific sites. Suppression of CAF-1 leads to differentiation of myeloid stem and progenitor cells into a mixed lineage state. These findings provide important insights into cell fate commitment and transcriptional regulation circuits.
NATURE COMMUNICATIONS
(2022)
Article
Immunology
Koichi Murakami, Haruka Sasaki, Akira Nishiyama, Daisuke Kurotaki, Wataru Kawase, Tatsuma Ban, Jun Nakabayashi, Satoko Kanzaki, Yoichi Sekita, Hideaki Nakajima, Keiko Ozato, Tohru Kimura, Tomohiko Tamura
Summary: IRF8 transcription factor regulates lineage choice in the myeloid cell system in a dose-dependent manner through epigenetic regulation of distinct sets of enhancers in cooperation with other transcription factors.
Article
Biology
Jung-Min Kim, Yeon-Suk Yang, Jaehyoung Hong, Sachin Chaugule, Hyonho Chun, Marjolein C. H. van Der Meulen, Ren Xu, Matthew B. Greenblatt, Jae-Hyuck Shim
Summary: Emerging evidence suggests that the ERK pathway in osteoblasts controls bone formation by suppressing the mTOR pathway, promoting mitochondrial function and SGK1 phosphorylation. While ERK inhibition blocks early differentiation of osteogenic precursors, it surprisingly promotes later stages of osteoblast differentiation, leading to enhanced bone formation. This study reveals a surprising dichotomy of ERK pathway functions in osteoblasts, where ERK activation promotes early differentiation but inhibits the subsequent differentiation via mTOR-mediated regulation of mitochondrial function and SGK1.
Article
Biochemistry & Molecular Biology
Jayanti Singh, Mohammad Sahil, Shamayeeta Ray, Criss Dcosta, Santosh Panjikar, G. Krishnamoorthy, Jagannath Mondal, Ruchi Anand
Summary: This study reveals the dynamic allosteric mechanism of NtrC proteins in sensing external signals and activating related pathways. It shows that phenol binding induces the rewiring of electrostatic connections and mutations can alter the conformation states and functions of the protein. Furthermore, it demonstrates that dynamic allosteric-driven conserved community networks are present and conserved across species.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Yeguang Hu, Daniela Salgado Figueroa, Zhihong Zhang, Margaret Veselits, Sourya Bhattacharyya, Mariko Kashiwagi, Marcus R. Clark, Bruce A. Morgan, Ferhat Ay, Katia Georgopoulos
Summary: The interplay between cohesin and CTCF generates a generic level of chromatin organization to limit promiscuous interactions between regulatory elements. However, a lineage-specific chromatin assembly is required to configure the genome for faithful lineage progression.
Article
Cell Biology
Lixiang Sun, Xiaowei Zhang, Shuai Wu, Youxi Liu, Christian F. Guerrero-Juarez, Wenjie Liu, Jinwen Huang, Qian Yao, Meimei Yin, Jiacheng Li, Raul Ramos, Yanhang Liao, Rundong Wu, Tian Xia, Xinyuan Zhang, Yichun Yang, Fengwu Li, Shujun Heng, Wenlu Zhang, Minggang Yang, Chi-Meng Tzeng, Chao Ji, Maksim V. Plikus, Richard L. Gallo, Ling-juan Zhang
Summary: By conducting single-cell RNA sequencing on mouse skin, researchers have classified dermal fibroblasts into different non-adipogenic and adipogenic cell states. They have identified IL-1-NF-kB and WNT-b-catenin signaling pathways as regulators of adipogenesis. Neutrophils and WNT activation play roles in wound-induced adipogenesis and lipolysis, respectively, while sustaining WNT activation inhibits adipogenesis and contributes to myofibroblast formation.
Article
Multidisciplinary Sciences
Dhurjhoti Saha, Solomon Hailu, Arjan Hada, Junwoo Lee, Jie Luo, Jeff A. Ranish, Yuan-chi Lin, Kyle Feola, Jim Persinger, Abhinav Jain, Bin Liu, Yue Lu, Payel Sen, Blaine Bartholomew
Summary: The SWI/SNF ATP-dependent chromatin remodeler, with its conserved AT-hook domain, is critical for regulating pluripotency, differentiation, and gene transcription. The AT-hook not only anchors chromatin modifiers to DNA but also regulates the intrinsic catalytic activity of SWI/SNF, leading to changes in ATP hydrolysis and nucleosome movement. The AT-hook is essential for SWI/SNF remodeling and activation of specific genes and enhancers in various cells.
NATURE COMMUNICATIONS
(2023)
Article
Environmental Sciences
Natsumi Fujiwara, Shohei Yamashita, Motoki Okamoto, Marion A. Cooley, Kazumi Ozaki, Eric T. Everett, Maiko Suzuki
Summary: In this study, it was found that perfluorooctanoic acid (PFOA) negatively affects tooth enamel development through cell death mechanisms involving necrosis/necroptosis and apoptosis, mediated by the ROS-MAPK/ERK signaling pathway. PFOA also suppressed cell proliferation and viability. This research provides initial evidence that PFOA could potentially contribute to cryptogenic enamel malformation.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2023)
Article
Computer Science, Artificial Intelligence
Qingtao Zhao, Jennie Si, Jian Sun
Summary: This work introduces a new event-driven dHDP method, which proves the UUB of system states and weights in networks, showing approximate control and cost functions approaching Bellman optimality. The algorithm is compared to the original time-driven dHDP to demonstrate its effectiveness.
IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS
(2022)
Article
Cell Biology
Pin Chen, Yanbing Lu, Binfeng He, Tao Xie, Chaolong Yan, Tengfei Liu, Silin Wu, Yuyang Yeh, Zeyang Li, Wei Huang, Xiaobiao Zhang
Summary: The expression of Rab32 is significantly upregulated in GBM and is positively correlated with tumor malignancy and poor prognosis. Knockdown of Rab32 attenuates the migration and invasion capability of GBM and suppresses the expression of invasion-related proteins and mesenchymal transition markers. Rab32 regulates ERK1/2/Drp1-dependent mitochondrial fission and promotes migration and invasion of GBM.
CELL DEATH & DISEASE
(2023)
Article
Chemistry, Multidisciplinary
Serena Arnaboldi, Gerardo Salinas, Aleksandar Karajic, Patrick Garrigue, Tiziana Benincori, Giorgia Bonetti, Roberto Cirilli, Sabrina Bichon, Sebastien Gounel, Nicolas Mano, Alexander Kuhn
Summary: One key method for designing bioinspired machines is transferring concepts from nature to man-made structures by integrating biomolecules into artificial mechanical systems, allowing the conversion of molecular information into macroscopic action. Hybrid bioelectrochemical swimmers can convert chiral information into enantiospecific macroscopic trajectories, with potential biomedical applications and food quality testing.
Article
Multidisciplinary Sciences
Jiayue Zhang, Yikui Gao, Di Liu, Jing-Shan Zhao, Jie Wang
Summary: This study investigates the three discharge domains in DC triboelectric nanogenerators and develops a model to explain the relationship between ideal conditions and real outputs, resulting in an increase in output power.
NATURE COMMUNICATIONS
(2023)
Article
Immunology
Tobias Strid, Kazuki Okuyama, Johanna Tingvall-Gustafsson, Jacob Kuruvilla, Christina T. Jensen, Stefan Lang, Mahadesh Prasad, Rajesh Somasundaram, Josefine Ahsberg, Susana Cristobal, Shamit Soneji, Jonas Ungerback, Mikael Sigvardsson
Summary: The development of B lymphocytes is influenced by the interaction between chromatin structure and lineage-specific transcription factors. Research indicates that during B lineage commitment, essential genes have transcriptional control elements with accessible chromatin, and binding sites for key regulators like EBF1 and PAX5 are predominantly in already accessible regions. This demonstrates the interplay between the epigenetic landscape and transcription factors in cell specification.
JOURNAL OF IMMUNOLOGY
(2021)
Article
Multidisciplinary Sciences
Kim Theilgaard-Monch, Sachin Pundhir, Kristian Reckzeh, Jinyu Su, Marta Tapia, Benjamin Furtwangler, Johan Jendholm, Janus Schou Jakobsen, Marie Sigurd Hasemann, Kasper Jermiin Knudsen, Jack Bernard Cowland, Anna Fossum, Erwin Schoof, Mikkel Bruhn Schuster, Bo T. Porse
Summary: This study reveals the regulatory mechanism of tissue-specific transcription factors in cell differentiation, which first launch an enhancer-primed differentiation program, then promote cell cycle exit by repressing MYC target gene expression and E2F-mediated gene expression, and by up-regulating Cdk1/2/4 inhibitors. Following cell cycle exit, the primed differentiation program is activated for terminal differentiation.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Yan Fung Wong, Yatendra Kumar, Martin Proks, Jose Alejandro Romero Herrera, Michaela Mrugala Rothova, Rita S. Monteiro, Sara Pozzi, Rachel E. Jennings, Neil A. Hanley, Wendy A. Bickmore, Joshua M. Brickman
Summary: Cell proliferation in embryonic development plays a crucial role in tissue expansion and the equilibration of gene regulatory networks for future differentiation. The expansion of lineage-specific intermediates is important for achieving high-fidelity in vitro differentiation. This research identifies a link between progenitor expansion and tissue-specific changes in the enhancer landscape using human embryonic stem cell-derived endodermal progenitors as a ventral foregut model.
NATURE CELL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Junil Kim, Michaela Mrugala Rothova, Esha Madan, Siyeon Rhee, Guangzheng Weng, Antonio M. Palma, Linbu Liao, Eyal David, Ido Amit, Morteza Chalabi Hajkarim, Vignesh Vudatha, Andres Gutierrez-Garcia, Eduardo Moreno, Robert Winn, Jose Trevino, Paul B. Fisher, Joshua M. Brickman, Rajan Gogna, Kyoung Jae Won
Summary: Development of multicellular organisms relies on persistent cell-cell communication, which drives lineage specification and cell fate decisions. The current single-cell RNA-seq technology lacks spatial information needed to analyze cell-cell contact-dependent gene expression. To overcome this, we performed RNA sequencing of physically interacting cells (PIC-seq) and compared them with single-cell transcriptomes from developing mouse embryos. Our analysis identified cell-type-dependent gene expression signatures, and we developed a computational model to predict the impact of one cell type on neighboring cell types. We also developed a spatial embedding method to visualize the distribution of cells in a 2D space. This innovative approach allows us to study contact-specific gene regulation during embryogenesis.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemical Research Methods
Anders H. Kverneland, Ole Ostergaard, Kristina Bennet Emdal, Inge Marie Svane, Jesper Velgaard Olsen
Summary: This study demonstrates that enrichment of extracellular vesicles (EVs) by ultracentrifugation can significantly increase the depth of the plasma proteome analysis. By optimizing the workflow, over two thousand proteins can be quantified in a short time using label-free quantification and data independent acquisition (DIA), enabling high-throughput analysis of plasma samples and supporting potential biomarker discovery in the future.
Review
Immunology
Giulia Franciosa, Anders H. Kverneland, Agnete W. P. Jensen, Marco Donia, Jesper V. Olsen
Summary: Cancer survival relies on tumor cells evading immune recognition, but immunotherapy has shown promising results in metastatic cancers. Resistance mechanisms limit efficacy, so understanding the interplay between immune cells and tumors is crucial. Mass spectrometry-based proteomics may provide insights into tumor immunity and cancer immunotherapies, allowing for translational and clinical discoveries.
SEMINARS IN IMMUNOPATHOLOGY
(2023)
Article
Cell Biology
Chanchal Chauhan, Ana Martinez-Val, Rainer Niedenthal, Jesper Velgaard Olsen, Alexey Kotlyarov, Simon Bekker-Jensen, Matthias Gaestel, Manoj B. Menon
Summary: The TNF receptor-interacting protein kinases (RIPK)-1 and 3 regulate cell death response pathways. RIPK1 determines cell survival or death by associating with distinct complexes, while RIPK3 is a target of PRMT5-mediated arginine dimethylation. This study uncovers PRMT5-mediated RIPK3 methylation as a novel modulator of RIPK1-dependent signaling.
CELL DEATH DISCOVERY
(2023)
Article
Chemistry, Analytical
Teeradon Phlairaharn, Zilu Ye, Elena Krismer, Anna-Kathrine Pedersen, Maik Pietzner, Jesper V. Olsen, Erwin M. Schoof, Brian C. Searle
Summary: A linear ion trap (LIT) is a cost-effective and robust mass spectrometer with fast scanning speed and high sensitivity. Its primary disadvantage is inferior mass accuracy compared to more commonly used time-of-flight or orbitrap (OT) mass analyzers. In this study, we demonstrate the potential versatility of the LIT as a stand-alone mass analyzer for low-input proteomics, including library generation. We optimized LIT data acquisition methods, performed library-free searches, and successfully generated matrix-matched calibration curves using only 10 ng of starting material.
ANALYTICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Fabiana Di Gianvincenzo, Cecil Krarup Andersen, Troels Filtenborg, Meaghan Mackie, Madeleine Ernst, Jazmin Ramos Madrigal, Jesper V. Olsen, Jorge Wadum, Enrico Cappellini
Summary: The application of mass spectrometry-based proteomics to artworks is valuable for characterizing protein-based materials and reconstructing the artwork's history. Proteomic analysis of Danish Golden Age canvas paintings identified cereal and yeast proteins, indicating the use of a beer brewing by-product as a binder, consistent with local artists' manuals. Metabolomic analysis supports these findings and suggests the use of drying oils. This study highlights the value of untargeted proteomics in correlating unconventional artistic materials with local culture.
Article
Psychology, Multidisciplinary
Luana Lemos Leao, Weslley Gomes de Araujo Valadares, Nayra Suze Souza e Silva, Stenio Fernando Pimentel Duarte, Alfredo Mauricio Batista de Paula, Desiree Sant'Ana Haikal, Sergio Henrique Sousa Santos, Jeane Soares, Joelton Cruz, Jordana Santos, Gustavo Leal Teixeira, Renato Sobral Monteiro-Junior
Summary: The COVID-19 pandemic has led to increased depression and other mental disorders in the general population, influenced by various individual and contextual factors. Physical activity interventions, both before and during the pandemic, are associated with a lower risk of depressive symptoms.
BEHAVIORAL SCIENCES
(2023)
Editorial Material
Biochemistry & Molecular Biology
Chiara Francavilla
Summary: Cells maintain homeostasis under stress conditions by minimizing damages, maintaining structural integrity, and modifying the activity of macromolecules and signaling molecules. The comprehensive understanding of how stress-regulated signaling pathways regulate cell survival is still elusive, but new research has provided some insights.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Tanveer S. Batth, Jonas L. Simonsen, Cristina Hernandez-Rollan, Soren Brander, Jens Preben Morth, Katja S. Johansen, Morten H. H. Norholm, Jakob B. Hoof, Jesper V. Olsen
Summary: The methyltransferase NHMT responsible for N-terminal histidine methylation modification is identified and validated through mass spectrometry-based proteomics and CRISPR/Cas9. NHMT protects LPMOs from auto-oxidative inactivation by methylating the His1 site. The biotechnological potential of recombinant production of proteins and peptides with this specific post-translational modification is demonstrated.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Ulises H. H. Guzman, Henriette Aksnes, Rasmus Ree, Nicolai Krogh, Magnus E. E. Jakobsson, Lars J. J. Jensen, Thomas Arnesen, Jesper V. V. Olsen
Summary: Protein N-terminal (Nt) acetylation is a common modification in eukaryotes and plays a crucial role in promoting stability of the proteome. However, the functional impact of Nt-acetylation has been hindered by its pleiotropic effects. In this study, we used proteomics approaches to analyze the effects of NatA deficiency in Saccharomyces cerevisiae and found that it leads to global proteome remodeling and decreased thermostability of ribosomes.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Teresa E. Knudsen, William B. Hamilton, Martin Proks, Maria Lykkegaard, Madeleine Linneberg-Agerholm, Alexander V. Nielsen, Marta Perera, Luna Lynge Malzard, Ala Trusina, Joshua M. Brickman
Summary: Cooperative DNA binding of transcription factors plays an important role in cell specification. NANOG and ESRRB are key transcription factors associated with pluripotency. When both factors are present, ESRRB supports pluripotency. However, in the absence of NANOG, ESRRB supports a bistable culture with characteristics of primitive endoderm. The quantitative relationship between NANOG and ESRRB allows for regulation of cell differentiation, and ESRRB activity safeguards plasticity.
Article
Biochemistry & Molecular Biology
Samuel Ogden, Ibrahim Ahmed, Shen-Hsi Yang, Paul Fullwood, Chiara Francavilla, Andrew D. Sharrocks
Summary: Esophageal adenocarcinoma (OAC) is a deadly disease with limited targeted therapies. In this study, the downstream pathways of ERBB2, which is frequently activated in OAC, were investigated using various molecular analyses. The findings suggest that dysregulated ERBB2 signaling in OAC is mediated at the transcriptional level by the transcription factor AP-1, which controls cell behavior and is associated with features of epithelial-mesenchymal transition (EMT). This study provides valuable insights into the molecular determinants underlying the aberrant behavior of OAC cells.