Article
Immunology
Gabriela K. Fragiadakis, Zachary B. Bjornson-Hooper, Deepthi Madhireddy, Karen Sachs, Han Chen, David R. McIlwain, Matthew H. Spitzer, Sean C. Bendall, Garry P. Nolan
Summary: Evaluating the health and competence of the immune system is crucial for assessing vaccine responses, autoimmune conditions, cancer prognosis, and treatment. This study used mass cytometry to analyze blood samples from 86 individuals and provide reference ranges for cell-specific immune markers, highlighting differences across sex and age. The researchers identified modules of immune features that suggest an underlying structure to the immune system based on signaling pathway responses across different cell types. The study also found distinct immune responses in males and females, with increased MAPK signaling in inflammatory pathways in innate immune cells and greater overall coordination of immune cell responses in females.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Harindra E. Amarasinghe, Ping Zhang, Justin P. Whalley, Alice Allcock, Gabriele Migliorini, Andrew C. Brown, Giuseppe Scozzafava, Julian C. Knight
Summary: This study investigates the epigenetic regulation in monocytes during innate immune activation, including acute response and endotoxin tolerance states. Differential gene expression, chromatin accessibility, and enhancer-derived RNA signatures were identified, with distinct patterns in endotoxin tolerance models. Integrating eQTL mapping and GWAS analysis revealed potential therapeutic targets for immunosuppression and diseases.
Article
Biodiversity Conservation
Jeroen Jansen, Jan Jansen, Abbey T. Dean, Robert Brandle, David E. Peacock, Menna E. Jones
Summary: A spatially balanced transect design was used to collect data on the distribution of European rabbits and create high-resolution distribution maps. The model suggested that the presence of rabbit warrens is influenced by geology, vegetation cover, and topographic wetness index, while the number of holes per warren depends on terrain ruggedness, vegetation cover, and prior destruction. The method showed high accuracy in predicting rabbit hole numbers and can be further improved in future studies.
JOURNAL OF APPLIED ECOLOGY
(2023)
Article
Multidisciplinary Sciences
C. Dominguez Conde, C. Xu, L. B. Jarvis, D. B. Rainbow, S. B. Wells, T. Gomes, S. K. Howlett, O. Suchanek, K. Polanski, H. W. King, L. Mamanova, N. Huang, P. A. Szabo, L. Richardson, L. Bolt, E. S. Fasouli, K. T. Mahbubani, M. Prete, L. Tuck, N. Richoz, Z. K. Tuong, L. Campos, H. S. Mousa, E. J. Needham, S. Pritchard, T. Li, R. Elmentaite, J. Park, E. Rahmani, D. Chen, D. K. Menon, O. A. Bayraktar, L. K. James, K. B. Meyer, N. Yosef, M. R. Clatworthy, P. A. Sims, D. L. Farber, K. Saeb-Parsy, J. L. Jones, S. A. Teichmann
Summary: This study investigated immune cells in 16 human tissues using single-cell RNA sequencing and VDJ sequencing, revealing the distribution of finely phenotyped immune cell types across tissues and uncovering tissue-specific features and clonal architecture of T and B cells.
Article
Biochemistry & Molecular Biology
Chae-Eun Moon, Yong Woo Ji, Jun-ki Lee, Kyusun Han, Hyunjin Kim, Seok Ho Byeon, Suenghan Han, Jinu Han, Yuri Seo
Summary: Uncovering region-specific changes in the myopic retina can provide clues to the pathogenesis of myopia progression. Proteomic analysis in this study suggested that oxidative stress can be the primary pathogenesis of myopia progression and that the far-periphery retina plays a role as the key responder. Antithrombin-III, fibrinogen gamma chain, and fibrinogen beta chain were identified as hub proteins for myopia progression, which were upregulated in the far-periphery retina.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Jill E. Moore, Xiao-Ou Zhang, Shaimae Elhajjajy, Kaili Fan, Henry E. Pratt, Fairlie Reese, Ali Mortazavi, Zhiping Weng
Summary: This study integrated experimentally validated data from various cell and tissue types to generate a collection of verified TSS annotations, updating TSS annotations for 20% of GENCODE genes and providing validated new candidate GWAS genes.
Article
Biochemical Research Methods
Kehui Liu, Shanjun Deng, Chang Ye, Zeqi Yao, Jianguo Wang, Han Gong, Li Liu, Xionglei He
Summary: SMALT is a substitution mutation-aided lineage-tracing system that outperforms available cell barcoding methods in mapping cell phylogeny. Utilizing SMALT in Drosophila melanogaster enables high-quality cell phylogenetic trees to be obtained.
Article
Cardiac & Cardiovascular Systems
Jiangming Sun, Pratibha Singh, Annelie Shami, Ewelina Kluza, Mengyu Pan, Djordje Djordjevic, Natasha Barascuk Michaelsen, Cecilia Kennback, Nicole N. van der Wel, Marju Orho-Melander, Jan Nilsson, Ivan Formentini, Karin Conde-Knape, Esther Lutgens, Andreas Edsfeldt, Isabel Goncalves
Summary: This study identifies the specific locations of atherosclerotic plaque ruptures in human carotid arteries and the underlying mechanisms. The proximal and most stenotic regions are found to be vulnerable to plaque rupture. RNA sequencing reveals differentially expressed genes that distinguish these regions, with matrix metallopeptidase 9 being associated with atherosclerosis risk. These findings provide insights for the development of targeted therapies against plaque rupture.
JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Sergio Triana, Megan L. Stanifer, Camila Metz-Zumaran, Mohammed Shahraz, Markus Mukenhirn, Carmon Kee, Clara Serger, Ronald Koschny, Diana Ordonez-Rueda, Malte Paulsen, Vladimir Benes, Steeve Boulant, Theodore Alexandrov
Summary: The study revealed that interferon controls human astrovirus infection and the virus can infect all major cell types and lineages in human intestinal organoids. Each intestinal epithelial cell lineage undergoes an antiviral transcriptional reprogramming by upregulating distinct sets of interferon-stimulated genes upon infection, indicating a unique role in resolving virus infection.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Yafen Wang, Zonggui Chen, Xiong Zhang, Xiaocheng Weng, Jikai Deng, Wei Yang, Fan Wu, Shaoqing Han, Chao Xia, Yu Zhou, Yu Chen, Xiang Zhou
Summary: This study presents a method for detecting f(5)C modifications in RNA and a transcriptome-wide f(5)C mapping technique called f(5)C-seq. Over 1000 f(5)C sites were identified in Saccharomyces cerevisiae using f(5)C-seq, and it was found that f(5)C has a preference for wobble sites in mRNA, suggesting its potential role in translation regulation.
ACS CHEMICAL BIOLOGY
(2022)
Article
Immunology
Rui Fan, Wenjun Que, Zhuoting Liu, Wei Zheng, Xia Guo, Linqi Liu, Fei Xiao
Summary: This study analyzed the changes in immune cell populations in myasthenia gravis (MG) patients and identified potential cellular biomarkers. The study also revealed abnormal expression of immune checkpoints in MG patients, providing a rationale for further investigation of immune checkpoint-related therapy.
CLINICAL IMMUNOLOGY
(2022)
Article
Immunology
Paul Haase, Simon Schaefer, Roman G. Gerlach, Thomas H. Winkler, David Voehringer
Summary: This study used a fate mapping approach to investigate the population dynamics of humoral immune response against helminths. The results demonstrated that a specific type of memory B cells persisted after the clearance of primary infection and played an important role in secondary infection.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Immunology
Veronika A. Myasoedova, Ilaria Massaiu, Donato Moschetta, Mattia Chiesa, Paola Songia, Vincenza Valerio, Valentina Alfieri, Romain Capoulade, Daniela Trabattoni, Daniele Andreini, Elvira Mass, Valentina Parisi, Paolo Poggio
Summary: The study found that aortic valve fibrosis in severe AS patients is sex-specific, with women exhibiting higher fibrotic tissue composition and lower aortic valve calcium content compared to men. Gene expression analysis showed that pro-fibrotic processes are predominant in women, while pro-inflammatory processes linked to the immune response system are enhanced in men. Cell type enrichment analysis revealed that mesenchymal cells are over-represented in stenotic aortic valves of women, while signatures for monocytes, macrophages, T and B cells are enriched in men.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Dexi Bi, Yin Zhu, Yaohui Gao, Hao Li, Xingchen Zhu, Rong Wei, Ruting Xie, Chunmiao Cai, Qing Wei, Huanlong Qin
Summary: This study identified Fusobacterium species and subspecies in CRC patient samples using a new sequencing method. They found that certain species are associated with CRC in tumor samples and feces. Additionally, different Fusobacterium lineages may play different functional roles in CRC.
NATURE COMMUNICATIONS
(2022)
Article
Environmental Sciences
Kai Cheng, Juanle Wang, Xinrong Yan
Summary: A forest type classification framework based on spectral, spatial, and temporal features was developed in this study, proving its effectiveness in various Chinese geographic regions and providing support for accurate forest management.
Article
Multidisciplinary Sciences
Matthew Zimmerman, Landry Blanc, Pei-Yu Chen, Veronique Dartois, Brendan Prideaux
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2018)
Article
Biochemical Research Methods
Mark R. Cronan, Molly A. Matty, Allison F. Rosenberg, Landry Blanc, Charlie J. Pyle, Scott T. Espenschied, John F. Rawls, Veronique Dartois, David M. Tobin
Article
Microbiology
Jansy Sarathy, Landry Blanc, Nadine Alvarez-Cabrera, Paul O'Brien, Isabela Dias-Freedman, Marizel Mina, Matthew Zimmerman, Firat Kaya, Hsin-Pin Ho Liang, Brendan Prideaux, Jillian Dietzold, Padmini Salgame, Radojka M. Savic, Jennifer Linderman, Denise Kirschner, Elsje Pienaar, Veronique Dartois
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2019)
Article
Multidisciplinary Sciences
Hassan Safi, Pooja Gopal, Subramanya Lingaraju, Shuyi Ma, Carly Levine, Veronique Dartois, Michelle Yee, Liping Li, Landry Blanc, Hsin-Pin Ho Liang, Seema Husain, Mainul Hoque, Patricia Soteropoulos, Tige Rustad, David R. Sherma, Thomas Dick, David Alland
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Immunology
Vincent Le Moigne, Anne-Laure Roux, Aude Jobart-Malfait, Landry Blanc, Karima Chaoui, Odile Burlet-Schiltz, Jean-Louis Gaillard, Stephane Canaan, Jerome Nigou, Jean-Louis Herrmann
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2020)
Review
Chemistry, Analytical
Michael Tuck, Landry Blanc, Rita Touti, Nathan Heath Patterson, Sebastiaan Van Nuffel, Sandrine Villette, Jean-Christophe Taveau, Andreas Rompp, Alain Brunelle, Sophie Lecomte, Nicolas Desbenoit
ANALYTICAL CHEMISTRY
(2021)
Article
Respiratory System
Pauline Esteves, Landry Blanc, Alexis Celle, Isabelle Dupin, Elise Maurat, Nivea Amoedo, Guillaume Cardouat, Olga Ousova, Lara Gales, Florian Bellvert, Hugues Begueret, Matthieu Thumerel, Jean-William Dupuy, Nicolas Desbenoit, Roger Marthan, Pierre-Olivier Girodet, Rodrigue Rossignol, Patrick Berger, Thomas Trian
Summary: This study reveals a metabolic shift towards mitochondrial 0-oxidation in asthmatic BSM cells, and identifies fatty acid metabolism as a new key target to reduce BSM remodelling in asthma.
EUROPEAN RESPIRATORY JOURNAL
(2021)
Article
Chemistry, Analytical
Landry Blanc, Gino B. Ferraro, Michael Tuck, Brendan Prideaux, Veronique Dartois, Rakesh K. Jain, Nicolas Desbenoit
Summary: Isotopic labeling is commonly used to decipher metabolism in living biological systems by providing labeled compounds as substrates, allowing for identification of metabolites using mass spectrometry. Utilizing mass spectrometry imaging (MSI) with a variation of the Kendrick analysis concept can rapidly detect heavy atom incorporation into metabolites. This processing method offers a new perspective to study metabolic networks without requiring advanced computational capabilities.
ANALYTICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Gianluca Sighinolfi, Samantha Clark, Landry Blanc, Daniela Cota, Boutayna Rhourri-Frih
Summary: Studies have shown that obesity is closely related to changes in brain structure and function. Through experiments on mice, it was found that a high-fat diet can rapidly alter the brain lipidome, with some changes persisting even after weight loss.
SCIENTIFIC REPORTS
(2021)
Review
Chemistry, Multidisciplinary
Michael Tuck, Florent Grelard, Landry Blanc, Nicolas Desbenoit
Summary: Multimodal imaging is a powerful strategy for combining information from multiple images, providing more comprehensive information and better reflecting the nature of tissues. This review focuses on the multimodal approaches of coupling Matrix-assisted Laser Desorption Ionization Mass Spectrometry Imaging (MALDI-MSI) with other imaging modalities.
FRONTIERS IN CHEMISTRY
(2022)
Meeting Abstract
Oncology
Gino Ferraro, Ahmed Ali, Alba Luengo, Amy Deik, Keene Abbott, Divya Bezwada, Landry Blanc, Brendan Prideaux, Xin Jin, Jessica Posada, Zohreh Amoozgar, Raphael Ferreira, Ivy Chen, Kamila Naxerova, Christopher Ng, Anna Westermark, Shawn Davidson, Dai Fukumura, Veronique Dartois, Clary Clish, Matthew Vander Heiden, Rakesh Jain
Meeting Abstract
Respiratory System
Pauline Esteves, Landry Blanc, Alexis Celle, Isabelle Dupin, Elise Maurat, Nivea Amoedo, Guillaume Cardouat, Olga Ousova, Lara Gales, Florian Bellvert, Hugues Begueret, Matthieu Thumerel, Pierre-Olivier Girodet, Rodrigue Rossignol, Patrick Berger, Thomas Trian
EUROPEAN RESPIRATORY JOURNAL
(2021)
Meeting Abstract
Oncology
Gino B. Ferraro, Ahmed Ali, Alba Luengo, David P. Kodack, Amy Deik, Keene L. Abbott, Divya Bezwada, Landry Blanc, Brendan Prideaux, Xin Jin, Jessica M. Possada, Jiang Chen, Christopher R. Chin, Zohreh Amoozgar, Raphael Ferreira, Ivy Chen, Kamila Naxerova, Christopher Ng, Anna M. Westermark, Mark Duquette, Sylvie Roberge, Costas A. Lyssiotis, Dan G. Duda, Todd R. Golub, Shawn M. Davidson, Dai Fukumura, Veronique A. Dartois, Clary B. Clish, Matthew G. Vander Heiden, Rakesh K. Jain
Article
Oncology
Gino B. Ferraro, Ahmed Ali, Alba Luengo, David P. Kodack, Amy Deik, Keene L. Abbott, Divya Bezwada, Landry Blanc, Brendan Prideaux, Xin Jin, Jessica M. Possada, Jiang Chen, Christopher R. Chin, Zohreh Amoozgar, Raphael Ferreira, Ivy X. Chen, Kamila Naxerova, Christopher Ng, Anna M. Westermark, Mark Duquette, Sylvie Roberge, Neal I. Lindeman, Costas A. Lyssiotis, Jens Nielsen, David E. Housman, Dan G. Duda, Elena Brachtel, Todd R. Golub, Lewis C. Cantley, John M. Asara, Shawn M. Davidson, Dai Fukumura, Veronique A. Dartois, Clary B. Clish, Rakesh K. Jain, Matthew G. Vander Heiden
Summary: Ferraro et al. found that fatty acid synthesis is crucial for brain cancer metastasis, and inhibiting this process can reduce the metastatic growth of breast cancer cells in the brain. Metabolic adaptations required for brain metastatic breast cancer growth may introduce vulnerabilities that can be exploited for therapy, as shown by differences in nutrient availability across metastatic sites.
Correction
Oncology
Gino B. Ferraro, Ahmed Ali, Alba Luengo, David P. Kodack, Amy Deik, Keene L. Abbott, Divya Bezwada, Landry Blanc, Brendan Prideaux, Xin Jin, Jessica M. Posada, Jiang Chen, Christopher R. Chin, Zohreh Amoozgar, Raphael Ferreira, Ivy X. Chen, Kamila Naxerova, Christopher Ng, Anna M. Westermark, Mark Duquette, Sylvie Roberge, Neal I. Lindeman, Costas A. Lyssiotis, Jens Nielsen, David E. Housman, Dan G. Duda, Elena Brachtel, Todd R. Golub, Lewis C. Cantley, John M. Asara, Shawn M. Davidson, Dai Fukumura, Veronique A. Dartois, Clary B. Clish, Rakesh K. Jain, Matthew G. Vander Heiden