Article
Multidisciplinary Sciences
Kaiwen Wang, Yuqiu Yang, Fangjiang Wu, Bing Song, Xinlei Wang, Tao Wang
Summary: While scRNA-seq data analysis techniques are advanced, research on CyTOF data analysis has lagged behind. Dimension reduction methods were benchmarked on real and synthetic CyTOF samples, highlighting the high level of complementarity between the methods. The study provides useful guidelines for choosing the appropriate method based on data structure and analytical needs.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Rashmi Kumar, Candace C. C. Liu, Sean C. Bendall, Michael Angelo
Summary: This study introduces a synthesis method of a dendrimer-based polymer and its application in MIBI-TOF tissue imaging. By comparing the staining performance of antibodies conjugated with dendrimers or linear polymers in FFPE tissue, it was found that dendrimers and linear polymers have comparable avidities. Moreover, dendrimers have advantages such as less background staining and no off-target binding in neural tissue. Overall, this research provides a versatile framework for using third-generation dendrimer-conjugated antibodies with improved staining compared to conventional linear polymers.
Article
Chemistry, Analytical
Ying Zhang, Bei Gao, Luis Valdiviez, Chao Zhu, Tara Gallagher, Katrine Whiteson, Oliver Fiehn
Summary: Stable isotope tracers are commonly used with gas chromatography coupled to mass spectrometry for enzyme activity and metabolic pathway studies. In this research, three commercially available instruments were used to analyze samples from a stable isotope labeling study on Rothia mucilaginosa metabolism. The study found that all three GC-MS instruments can be used for stable isotope tracing studies, with high-resolution GC-QTOF MS offering additional capabilities in identifying the chemical structures of unknown compounds.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Tao Tang, Xun Liu, Yapeng Yuan, Ryota Kiya, Yigang Shen, Tianlong Zhang, Kengo Suzuki, Yo Tanaka, Ming Li, Yoichiroh Hosokawa, Yaxiaer Yalikun
Summary: This study presents a label-free and cost-effective method for analyzing microalgal single-cells at subcellular resolution using impedance cytometry. It demonstrates the relationships between impedance signals and submicron intracellular components for the first time. By tracking changes in biophysical properties through electrical diameter and morphology metrics, the study provides insights into how submicron intracellular components and cell morphology affect impedance signals.
Article
Biochemical Research Methods
Aleksandra A. Petelski, Edward Emmott, Andrew Leduc, R. Gray Huffman, Harrison Specht, David H. Perlman, Nikolai Slavov
Summary: The study introduces the SCoPE2 protocol for single-cell protein analysis, which utilizes isobaric mass tags for labeling and achieves cost-effective quantitative protein analysis.
Article
Chemistry, Analytical
Claudia Ctortecka, Karel Stejskal, Gabriela Krssakova, Sasha Mendjan, Karl Mechtler
Summary: Advancements in single-cell proteomics workflows have enhanced sensitivity and reproducibility for characterizing unknown biological phenomena. The introduction of multiplexed single-cell proteomics has led to a trend of combining single-cell measurements with abundant carriers to improve precursor selection and identification accuracy, although extreme carrier spikes may affect quantitative accuracy. Narrowly titrated carrier spikes have been found to provide comparable sensitivity with superior accuracy, while alternative multiplexing strategies can help evaluate data quality. Ultimately, optimized experimental designs for multiplexed proteomics of trace samples can lead to improved quantitative accuracy and elevated replicate overlap.
ANALYTICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Chen Chen, Zhilun Zhao, Naixin Qian, Shixuan Wei, Fanghao Hu, Wei Min
Summary: The research team developed a multi-parameter measurement system that can simultaneously quantify cell surface proteins, endocytosis activities, and metabolic dynamics of single live cells. This technique allows for analysis of 14 parameters under drug perturbations, enabling powerful clustering, correlation, and network analysis.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Analytical
Florent Penen, Rene Raave, Annemarie Kip, Sandra Heskamp, Per Malmberg
Summary: ToF-SIMS imaging is a quick and sensitive technique that can visualize HER2 specific radiotracers in ovarian and breast cancer xenograft tumor sections to reflect the heterogeneous distribution of trastuzumab.
MICROCHEMICAL JOURNAL
(2022)
Review
Biochemical Research Methods
Shuting Xu, Huwei Liu, Yu Bai
Summary: Immunoassay is a crucial clinical technique for disease diagnosis. Mass spectrometry immunoassays (MSIAs) have become popular due to their powerful readout capabilities and improved sensitivity through the development of mass labels. MSIAs have expanded from element-based methods to laser-based and ambient MS, offering high potential for clinical applications such as biomarker screening and single-cell analysis.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Michael J. Geuenich, Jinyu Hou, Sunyun Lee, Shanza Ayub, Hartland W. Jackson, Kieran R. Campbell
Summary: Astir is a probabilistic model that assigns cells to cell types by integrating prior knowledge of marker proteins, enabling annotations at the million-cell scale with scalability and robustness.
Article
Chemistry, Analytical
Yanrong Wen, Jialing Zhao, Hui He, Quan Zhao, Zhen Liu
Summary: The study introduces a new approach for simultaneously detecting multiple signaling proteins in individual living cells with high sensitivity. By applying this method, researchers discovered an imbalance between survival and apoptotic signaling outputs after EGFR pathway inactivation, which contributed to the final fate of the cell.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Xiaoxue Wu, Zhen Li, Jinian Shu, Zhongbing Lu, Junling Gao, Bo Yang, Kui Jiang, Yedong Guo, Jingyun Huang
Summary: By analyzing the exhaled breath of mice using a newly developed AI-TOFMS method, it was found that acrolein, ethanol, nitric oxide, and ammonia are potential exhaled biomarkers for pulmonary fibrosis.
Article
Chemistry, Analytical
Junho Park, Fengchao Yu, James M. Fulcher, Sarah M. Williams, Kristin Engbrecht, Ronald J. Moore, Geremy C. Clair, Vladislav Petyuk, Alexey I. Nesvizhskii, Ying Zhu
Summary: To overcome the issue of ratio compression in isobaric labeling-based multiplexed single-cell proteomics, we developed an improved MS3-based method using a linear ion trap. This method increased proteome coverage for single-cell-level peptides and was applied to study immune activation in single macrophages.
ANALYTICAL CHEMISTRY
(2023)
Review
Cell Biology
Reema Baskar, Sam C. Kimmey, Sean C. Bendall
Summary: Mass cytometry is a recent technology that allows sensitive quantification of the single-cell abundance of metal-isotope-tagged affinity reagents to key proteins, RNA, and peptides. It offers a robust way to analyze the dynamics of cellular regulation across multiple conditions and sample types in a single experiment.
TRENDS IN CELL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Allwin D. McDonald, Peyton M. Higgins, Andrew R. Buller
Summary: SUMS, a method for measuring enzyme activity, can be used to engineer enzymes for a wider range of substrates. This study develops principles for designing and interpreting SUMS assays, providing valuable information for improving enzyme activity, identifying variants, and determining mutational hot-spots.
NATURE COMMUNICATIONS
(2022)
Article
Urology & Nephrology
Insa M. Schmidt, Mia R. Colona, Bryan R. Kestenbaum, Leonidas G. Alexopoulos, Ragnar Palsson, Anand Srivastava, Jing Liu, Isaac E. Stillman, Helmut G. Rennke, Vishal S. Vaidya, Haojia Wu, Benjamin D. Humphreys, Sushrut S. Waikar
Summary: Analysis of gene expression profiles and the development of Luminex-based assays were used to identify promising non-invasive biomarkers of kidney fibrosis. CDH11, SMOC2, and PEDF were found to be associated with the severity of interstitial fibrosis and tubular atrophy, as well as progression to end-stage kidney disease in independent cohorts of chronic kidney disease patients.
KIDNEY INTERNATIONAL
(2021)
Article
Urology & Nephrology
Catherine R. Butler, Paul S. Appelbaum, Heather Ascani, Mark Aulisio, Catherine E. Campbell, Ian H. de Boer, Ashveena L. Dighe, Daniel E. Hall, Jonathan Himmelfarb, Richard Knight, Karla Mehl, Raghavan Murugan, Sylvia E. Rosas, John R. Sedor, John F. O'Toole, Katherine R. Tuttle, Sushrut S. Waikar, Michael Freeman
Summary: This article emphasizes the importance of critically examining the ethical basis of human subjects research involving some risks without anticipated clinical benefits. It provides a comprehensive conceptualization of the types of benefits that may be important to research participants and proposes a model to better respect and support participants in future research.
AMERICAN JOURNAL OF KIDNEY DISEASES
(2022)
Article
Biochemical Research Methods
Michael Y. Lee, Jacob S. Bedia, Salil S. Bhate, Graham L. Barlow, Darci Phillips, Wendy J. Fantl, Garry P. Nolan, Christian M. Schuerch
Summary: CellSeg is a powerful cell segmentation software for analyzing highly multiplexed tissue images that is accessible to biology researchers of any programming skill level.
BMC BIOINFORMATICS
(2022)
Article
Allergy
Tsuguhisa Nakayama, Ivan T. Lee, Wei Le, Yasuhiro Tsunemi, Nicole A. Borchard, David Zarabanda, Sachi S. Dholakia, Philip A. Gall, Angela Yang, Dayoung Kim, Makoto Akutsu, Takashi Kashiwagi, Zara M. Patel, Peter H. Hwang, Daniel N. Frank, Shin-ichi Haruna, Vijay R. Ramakrishnan, Garry P. Nolan, Sizun Jiang, Jayakar Nayak
Summary: There are inflammatory characteristic differences between White/non-Asian patients and Japanese patients with chronic rhinosinusitis with nasal polyps (CRSwNP). Both racial groups exhibit the same two major endotypes of the disease, but with differing ratios. Different inflammatory and epithelial cells contribute to these inflammatory profiles.
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2022)
Article
Biochemical Research Methods
John W. Hickey, Elizabeth K. Neumann, Andrea J. Radtke, Jeannie M. Camarillo, Rebecca T. Beuschel, Alexandre Albanese, Elizabeth McDonough, Julia Hatler, Anne E. Wiblin, Jeremy Fisher, Josh Croteau, Eliza C. Small, Anup Sood, Richard M. Caprioli, R. Michael Angelo, Garry P. Nolan, Kwanghun Chung, Stephen M. Hewitt, Ronald N. Germain, Jeffrey M. Spraggins, Emma Lundberg, Michael P. Snyder, Neil L. Kelleher, Sinem K. Saka
Summary: Recent developments in multiplexed protein imaging methods have provided detailed spatial and functional maps of complex tissues, utilizing antibodies against protein biomarkers. Key considerations for training future users, generating molecular tools, validating antibody panels, and harmonizing datasets are essential as these approaches become more widely adopted. This Perspective offers guidance for robust and reproducible antibody-based highly multiplexed tissue imaging.
Article
Biochemistry & Molecular Biology
Salil S. Bhate, Graham L. Barlow, Christian M. Schurch, Garry P. Nolan
Summary: A schematic of a biological system can help understand its organization and changes in pathology or evolution. Researchers have developed a computational approach to construct tissue schematics and interpret them using high-parameter imaging data and a biological model. Applying this approach to human lymphoid tissue and the tumor microenvironment in colorectal cancer revealed potential relay zones and mutations associated with patient survival.
Article
Immunology
Sizun Jiang, Chi Ngai Chan, Xavier Rovira-Clave, Han Chen, Yunhao Bai, Bokai Zhu, Erin McCaffrey, Noah F. Greenwald, Candace Liu, Graham L. Barlow, Jason L. Weirather, John Paul Oliveria, Tsuguhisa Nakayama, Ivan T. Lee, Matthias S. Matter, Anne E. Carlisle, Darci Philips, Gustavo Vazquez, Nilanjan Mukherjee, Kathleen Busman-Sahay, Michael Nekorchuk, Margaret Terry, Skyler Younger, Marc Bosse, Janos Demeter, Scott J. Rodig, Alexandar Tzankov, Yury Goltsev, David Robert McIlwain, Michael Angelo, Jacob D. Estes, Garry P. Nolan
Summary: Understanding the mechanisms of HIV tissue persistence requires the ability to visualize tissue microenvironments where infected cells reside. However, technological limitations hinder our ability to dissect the cellular components of HIV reservoirs. In this study, a protein and nucleic acid in situ imaging (PANINI) technique was developed to simultaneously quantify DNA, RNA, and protein levels within tissue compartments. By combining PANINI with multiplexed ion beam imaging (MIBI), over 30 parameters could be measured simultaneously. This technology enables the spatial dissection of cellular phenotypes, functional markers, and viral events resulting from infection, providing a framework for studying tissue responses in other infectious diseases and tumor biology.
Article
Urology & Nephrology
Rajasree Menon, Andrew S. Bomback, Blue B. Lake, Christy Stutzke, Stephanie M. Grewenow, Steven Menez, Vivette D. D'Agati, Sanjay Jain
KIDNEY INTERNATIONAL
(2022)
Editorial Material
Biochemical Research Methods
Denis Schapiro, Clarence Yapp, Artem Sokolov, Sheila M. Reynolds, Yu-An Chen, Damir Sudar, Yubin Xie, Jeremy Muhlich, Raquel Arias-Camison, Sarah Arena, Adam J. Taylor, Milen Nikolov, Madison Tyler, Jia-Ren Lin, Erik A. Burlingame, Young H. Chang, Samouil L. Farhi, Vesteinn Thorsson, Nithya Venkatamohan, Julia L. Drewes, Dana Pe'er, David A. Gutman, Markus D. Herrmann, Nils Gehlenborg, Peter Bankhead, Joseph T. Roland, John M. Herndon, Michael P. Snyder, Michael Angelo, Garry Nolan, Jason R. Swedlow, Nikolaus Schultz, Daniel T. Merrick, Sarah A. Mazzili, Ethan Cerami, Scott J. Rodig, Sandro Santagata, Peter K. Sorger
Summary: The imminent release of tissue atlases combining multichannel microscopy with single-cell sequencing and other omics data from normal and diseased specimens calls for data and metadata standards to guide data deposition, curation and release. The Minimum Information about Highly Multiplexed Tissue Imaging (MITI) standard, derived from best practices in genomics and microscopy, is introduced for highly multiplexed tissue images and traditional histology.
Article
Multidisciplinary Sciences
Amit Singh, Matthew H. Spitzer, Jaimy P. Joy, Mary Kaileh, Xiang Qiu, Garry P. Nolan, Ranjan Sen
Summary: Contrary to the traditional view, B lymphocytes can undergo multiple rounds of cell division independent of mitogens after the first mitosis, possibly due to unique characteristics of the postmitotic G1 phase resembling S and G2/M phases. Additionally, the expression of the Birc5 protein in the G1 phase of divided B cells plays a crucial role in apoptosis and rapid proliferation during B cell proliferation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Immunology
Zachary B. Bjornson-Hooper, Gabriela K. Fragiadakis, Matthew H. Spitzer, Han Chen, Deepthi Madhireddy, Kevin Hu, Kelly Lundsten, David R. McIlwain, Garry P. Nolan
Summary: Animal models play an important role in drug development and evaluation, but they imperfectly reflect human immunological behavior. In this study, we measured immune cell signaling responses in humans and several model organisms using mass cytometry and identified differences in cellular phenotypes and immune signaling events between species.
FRONTIERS IN IMMUNOLOGY
(2022)
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
Neurosciences
Akila Weerasekera, Adrian Ion-Margineanu, Garry Nolan, Maria Mody
Summary: Autism spectrum disorder (ASD) and schizophrenia (SZ) are neuropsychiatric disorders that have similar symptoms associated with social-cognitive impairment. This study compared subcortical volumes between adults with ASD, SZ, and neurotypicals (NT) and found overlapping abnormalities in subcortical structures between ASD and SZ. There were volume differences specific to ASD and SZ, such as in the left pallidum and left thalamus in ASD and in the right amygdala in SZ. The study also observed correlations between subcortical volumes and behavioral measures in the NT group, but not in the disorder groups.
Review
Oncology
Marc-A Baertsch, Garry P. Nolan, John W. Hickey
Summary: The complex determinants of health and disease can be understood by studying the rules of multicellular structure formation. Multiplexed imaging technology connects information across different biological scales, enabling the discovery of such rules and driving the development of new diagnostics and therapeutics.
Review
Cell Biology
Mythreye Venkatesan, Harini Mohan, Justin R. Ryan, Christian M. Schurch, Garry P. Nolan, David H. Frakes, Ahmet F. Coskun
Summary: 3D visualization technologies such as VR, AR, and MR have become popular in various domains due to their accessibility and affordability, creating an immersive experience and overcoming traditional 2D display constraints.
CELL REPORTS MEDICINE
(2021)