Article
Biochemistry & Molecular Biology
Marianna Avitabile, Ferdinando Bonfiglio, Vincenzo Aievola, Sueva Cantalupo, Teresa Maiorino, Vito Alessandro Lasorsa, Cinzia Domenicotti, Barbara Marengo, Heger Zbynek, Adam Vojtech, Achille Iolascon, Mario Capasso
Summary: The study reveals the association between intratumor heterogeneity (ITH) and drug resistance in high-risk neuroblastoma (NB). Different cell populations characterized by genes involved in various biological processes can contribute to the failure of NB drug treatment. Single-cell RNA sequencing analysis allows the identification of tumor heterogeneity and the discovery of clusters associated with worse/better survival.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Genetics & Heredity
Giorgio Milazzo, Giovanni Perini, Federico M. Giorgi
Summary: This study identified a global senescence signature and reduced proliferation in NBL cells treated with panobinostat, as well as transcriptional responses compatible with early neuronal differentiation. Through master regulator analysis, BAZ1A, HCFC1, MAZ, and ZNF146 were identified as the transcriptional regulators most significantly repressed by panobinostat, and experimental silencing confirmed their role in sustaining NBL cell proliferation in vitro.
Article
Multidisciplinary Sciences
Monika Graf, Marta Interlandi, Natalia Moreno, Dorthe Holdhof, Carolin Gobel, Viktoria Melcher, Julius Mertins, Thomas K. Albert, Dennis Kastrati, Amelie Alfert, Till Holsten, Flavia de Faria, Michael Meisterernst, Claudia Rossig, Monika Warmuth-Metz, Johannes Nowak, Gerd Meyer zu Horste, Chloe Mayere, Serge Nef, Pascal Johann, Michael C. Fruhwald, Martin Dugas, Ulrich Schuller, Kornelius Kerl
Summary: This study investigates the origin of rhabdoid tumors (RT) and identifies distinct cells of origin for the SHH and MYC subgroups of RT. It also reveals the epigenetic imbalance in MYC tumors and the effectiveness of the DNA demethylating agent decitabine in inhibiting tumor growth.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Julia Steger, Alison G. Cole, Andreas Denner, Tatiana Lebedeva, Grigory Genikhovich, Alexander Ries, Robert Reischl, Elisabeth Taudes, Mark Lassnig, Ulrich Technau
Summary: Using single-cell RNA sequencing in the cnidarian Nematostella vectensis, researchers have discovered that neurons, stinging cells, and gland cells originate from a common multipotent progenitor population. They also identified the conserved transcription factor gene SoxC as a key regulator of all neuroglandular lineages. Unlike vertebrates, the differentiation of neuroglandular cells in the sea anemone is maintained throughout all life stages and follows the same molecular trajectories.
Article
Clinical Neurology
Kicheol Kim, Anne-Katrin Probstel, Ryan Baumann, Julia Dyckow, James Landefeld, Elva Kogl, Lohith Madireddy, Rita Loudermilk, Erica L. Eggers, Sneha Singh, Stacy J. Caillier, Stephen L. Hauser, Bruce A. C. Cree, Ucsf MS-EPIC Team, Lucas Schirmer, Michael R. Wilson, Sergio E. Baranzini
Summary: The study identified differentially expressed genes in CD4+ T cells, monocytes, and CD8+ T cells of patients with multiple sclerosis, revealing an upregulation of NEDD8 activating enzyme-related genes in CD4+ T cells. Inhibition of NEDD8 activating enzyme significantly ameliorated disease severity in murine experimental autoimmune encephalomyelitis, suggesting neddylation as a crucial pathway in the pathogenesis of multiple sclerosis with potential implications for tailored disease-modifying agents.
Article
Clinical Neurology
Kicheol Kim, Anne-Katrin Proebstel, Ryan Baumann, Julia Dyckow, James Landefeld, Elva Kogl, Lohith Madireddy, Rita Loudermilk, Erica L. Eggers, Sneha Singh, Stacy J. Caillier, Stephen L. Hauser, Bruce A. C. Cree, Lucas Schirmer, Michael R. Wilson, Sergio E. Baranzini
Summary: This study identified differential gene expression in specific cell types of patients with multiple sclerosis, revealing the critical role of NEDD8 activating enzyme in CD4+ T cells and its association with disease progression. Inhibition of NEDD8 activating enzyme significantly ameliorated disease severity in murine experimental autoimmune encephalomyelitis, suggesting a potential therapeutic target for tailored disease-modifying agents.
Article
Oncology
Michele Simbolo, Giovanni Centonze, Luca Giudice, Federica Grillo, Patrick Maisonneuve, Anastasios Gkountakos, Chiara Ciaparrone, Laura Cattaneo, Giovanna Sabella, Rosalba Giugno, Paola Bossi, Paola Spaggiari, Alessandro Del Gobbo, Stefano Ferrero, Luca Mastracci, Alessandra Fabbri, Martina Filugelli, Giovanna Garzone, Natalie Prinzi, Sara Pusceddu, Adele Testi, Valentina Monti, Luigi Rolli, Alessandro Mangogna, Luisa Bercich, Mauro Roberto Benvenuti, Emilio Bria, Sara Pilotto, Alfredo Berruti, Ugo Pastorino, Carlo Capella, Maurizio Infante, Michele Milella, Aldo Scarpa, Massimo Milione
Summary: This study provides an integrated molecular analysis of 44 combined large cell neuroendocrine carcinomas (CoLCNECs), revealing that CoLCNECs are an independent histologic category with specific genomic and transcriptomic features that are different from other lung cancers. The findings of this study contribute to a better understanding of these rare tumors and may lead to the development of new diagnostic approaches for personalized treatments in CoLCNECs.
Article
Biology
Bas Molenaar, Louk T. Timmer, Marjolein Droog, Ilaria Perini, Danielle Versteeg, Lieneke Kooijman, Jantine Monshouwer-Kloots, Hesther de Ruiter, Monika M. Gladka, Eva van Rooij
Summary: Molenaar et al. used single-cell RNA sequencing to study gene expression changes in cardiac cells following ischemic injury, revealing that cardiomyocytes secrete B2M to promote scar formation. This data may offer insights for identifying therapeutic targets for cardiac repair.
COMMUNICATIONS BIOLOGY
(2021)
Article
Veterinary Sciences
Jian Zhang, Yan Cui
Summary: This study is the first to investigate the regulation of ferroptosis-related genes by hypoxia in yak and identified important genes and pathways. The findings provide valuable transcriptome data for understanding hypoxia adaptation.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Article
Cell Biology
Kevin Perez, Serban Ciotlos, Julia McGirr, Chandani Limbad, Ryosuke Doi, Joshua P. Nederveen, Mats Nilsson, Daniel A. Winer, William Evans, Mark Tarnopolsky, Judith Campisi, Simon Melov
Summary: The study reveals that muscle aging is associated with various factors such as inflammation, muscle stem cell depletion, mitochondrial dysfunction, and loss of motor neurons. Transcriptome profiling identifies changes in gene expression related to age and frailty, including key genes like MYH8, PDK4, and IGFN1. Additionally, a subpopulation expressing CDKN1A in aged samples suggests cellular senescence driven by p21(cip1). These findings provide valuable insights into age-related muscle loss and can guide the development of therapeutic strategies.
Article
Biochemistry & Molecular Biology
Daniele Mercatelli, Nicola Balboni, Alessandro Palma, Emanuela Aleo, Pietro Paolo Sanna, Giovanni Perini, Federico Manuel Giorgi
Summary: The study investigated two cell lines, BE2C and Kelly, of neuroblastoma, showing distinct transcriptional network activities with BE2C having more mesenchymal characteristics compared to Kelly. Single-cell data revealed that MYCN is not constantly active in these cells, and highlighted higher variance in metallothionein transcripts in Kelly cells.
Article
Microbiology
Alexa R. Cohn, Renato H. Orsi, Laura M. Carroll, Ruixi Chen, Martin Wiedmann, Rachel A. Cheng
Summary: Through transcriptomic comparisons using RNA-seq, this study revealed differences in gene transcription abundance and expression levels of pathogenic islands among NTS serovars, highlighting potential transcriptional mechanisms that facilitate the survival and adaptation of S. Cerro and S. Javiana in their respective hosts, impacting their disease-causing abilities in others. The study also demonstrated the utility of omics approaches in understanding the diversity of metabolic and virulence mechanisms among different NTS serovars.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Cell Biology
Myret Ghabriel, Ahmed El Hosseiny, Ahmed Moustafa, Asma Amleh
Summary: This study identified six members of the proteasome degradation system as potential stemness-related markers in mesenchymal stromal/stem cells (MSCs) derived from different tissues. The gene expression profile of these markers accurately validated the identity of MSCs across various tissue sources. Furthermore, a possible connection between these markers and antioxidant enzymes in MSC antioxidant defense system suggests their potential role in prolonging the lifespan of MSCs.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Developmental Biology
Austin Seroka, Sen-Lin Lai, Chris Q. Doe
Summary: This study uses single cell RNA sequencing of Drosophila embryos to identify genes that characterize different cell and tissue types during development. The research reveals coordinated changes in gene expression within each tissue and shows that neurons within a lineage are diverse, with neurons that share similar transcriptional profiles distributed among multiple lineages.
DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Feng Yang, Xutao Chen, Hui Zhang, Guo-Dong Zhao, Huifei Yang, Jiang Qiu, Siyan Meng, Penghan Wu, Liang Tao, Qin Wang, Gang Huang
Summary: BK polyomavirus (BKPyV) infection has a significant impact on the prognosis of kidney transplant recipients, but effective antiviral treatment is currently lacking. This study demonstrated the renal-cell-type tropism of BKPyV, with proximal tubule cells being the most susceptible. Furthermore, the study identified potential antiviral targets and provided insights for the development of new treatment strategies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Cell Biology
Alek G. Erickson, Polina Kameneva, Igor Adameyko
Summary: Since its discovery by His in 1850, the neural crest has been extensively studied for its crucial role in vertebrate development. Understanding the function and regulation of neural crest cell differentiation has made it an important model system in stem cell biology. Recent advancements in single cell multi-omics, statistical modeling, and developmental biology have provided valuable insights into the intriguing questions surrounding neural crest cells.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2023)
Article
Neurosciences
Leonie von Berlin, Jakub Orzechowski Westholm, Michael Ratz, Jonas Frisen
Summary: This article reports that hippocampal adult neural stem cells are derived from progeny of the neuroepithelial lineage during murine brain development. By analyzing thousands of clonally related cells using single-cell RNA-seq of barcoded clones, the researchers found evidence of early fate restriction of neuroepithelial stem cells to either neurogenic progenitor cells or non-neurogenic oligodendrogenic fate supplying cells for different hippocampal regions. This study provides new insights into the phenomenon of early fate restriction guiding the development of postnatal hippocampal neurogenesis.
Article
Developmental Biology
Aliia Murtazina, Igor Adameyko
Summary: The peripheral nervous system is a heterogeneous system with diverse functions, including communication between the brain and the body, control of development and regeneration. It can be divided into sensory, motor, autonomic and enteric domains. Recent advances in single-cell transcriptomics have revealed new neuronal subtypes and improved cell-type classifications. This article discusses the roles, origin and heterogeneity of the peripheral nervous system, highlighting recent discoveries and future perspectives.
Editorial Material
Gastroenterology & Hepatology
Emma R. R. Andersson
LIVER INTERNATIONAL
(2023)
Article
Multidisciplinary Sciences
Kazunori Sunadome, Alek G. G. Erickson, Delf Kah, Ben Fabry, Csaba Adori, Polina Kameneva, Louis Faure, Shigeaki Kanatani, Marketa Kaucka, Ivar Dehnisch Ellstroem, Marketa Tesarova, Tomas Zikmund, Jozef Kaiser, Steven Edwards, Koichiro Maki, Taiji Adachi, Takuya Yamamoto, Kaj Fried, Igor Adameyko
Summary: The developing skeleton produces mechanical tension that guides the directional outgrowth of skeletal muscles. Formation of oriented myofibrils is crucial in musculoskeletal development. The mechanisms that control myocyte orientation and fusion for muscle directionality in adults are still unknown.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Darya Krupenko, Aleksei Miroliubov, Emil Kryukov, Louis Faure, Ryo Minemizu, Lars Haag, Magnus Lundgren, Polina Kameneva, Maria Eleni Kastriti, Igor Adameyko
Summary: Parasitic flatworms have evolved various strategies, such as mimicking prey, to survive and transmit within hosts. This article describes the formation of a mimicry colony composed of different morphotypes of cercariae, and their functional specialization. The analysis of ribosomal sequences indicates that these cercariae belong to the digenean family Acanthocolpidae, likely genus Pleorchis. This discovery provides insight into the cooperative behavior of morphologically and functionally heterogeneous individuals for infection.
Article
Developmental Biology
Priti Agarwal, Clotilde Cadart, Loic Fort, James Gahan, Leah Greenspan, Thomas Juan, Polina Kameneva, Yuchuan Miao
Summary: This article introduces Development's "Pathway to Independence (PI) Programme," which aims to support postdocs in transitioning to their first independent positions. Furthermore, it presents the perspectives of eight PI Fellows on the future of developmental biology, providing insights into the current state and open questions in the field.
Article
Genetics & Heredity
Teng Gao, Maria Eleni Kastriti, Viktor Ljungstrom, Andreas Heinzel, Arthur S. Tischler, Rainer Oberbauer, Po-Ru Loh, Igor Adameyko, Peter J. Park, Peter V. Kharchenko
Summary: This study investigates mosaic chromosomal alterations (mCAs) in various human tissues and finds that approximately a quarter of healthy individuals carry clonally-expanded mCAs in at least one tissue, with varying prevalence and patterns across different tissue types.
Article
Biochemistry & Molecular Biology
David M. Kosek, Elnaz Banijamali, Walter Becker, Katja Petzold, Emma R. Andersson
Summary: This study investigates the combined effect of 3'-pairing and secondary structures in mRNAs on miRNA repression efficiency. The results show that 3'-pairing can compensate for low seed-binding site accessibility and enable repression of otherwise ineffective sites. The study also reveals that miRNA 3'-pairing regions can base-pair with nucleotides far upstream of the seed-binding site and tolerate both hairpins and unstructured bulges within the target site.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Gastroenterology & Hepatology
Afshan Iqbal, Noemi Van Hul, Lenka Belicova, Agustin A. Corbat, Simona Hankeova, Emma R. Andersson
Summary: In patients with Alagille syndrome and Jag1(Ndr/Ndr) mice, the intrahepatic bile ducts in the liver show distinct architectural differences in different regions. Insulin-like Growth Factor 1 (IGF1) has the potential to improve biliary outcomes, particularly in the peripheral bile ducts.
LIVER INTERNATIONAL
(2023)
Article
Biochemical Research Methods
Louis Faure, Ruslan Soldatov, Peter Kharchenko, Igor Adameyko
Summary: scFates is an extensive toolset for analyzing dynamic trajectories, including tree learning, feature association testing, branch differential expression, with a focus on cell biasing and fate splits at the level of bifurcations. It is designed to be fully integrated into the scanpy ecosystem for seamless analysis of trajectories from single-cell data of various modalities (e.g., RNA and ATAC).