Article
Cell Biology
Estefania Silveyra, Ronell Bologna-Molina, Rogelio Gonzalez-Gonzalez, Miguel Arocena
Summary: This study utilized confocal microscopy to investigate tissue architecture in oral squamous cell carcinoma and found that the staining pattern of wheat germ agglutinin can indicate the degree of cell cohesion, which decreases notably in invasive tumor clusters. Wheat germ agglutinin staining in combination with confocal microscopy may constitute a valuable tool for studying tissue architecture in oral cancer.
Article
Biochemistry & Molecular Biology
Kang Wang, Yuxin Yu, Yinhui Xu, Yingzi Yue, Fang Zhao, Wenyang Feng, Yijie Duan, Weicheng Duan, Jingjing Yue, Zhiyun Liao, Peng Fei, Hui Sun, Bo Xiong
Summary: Fluorescence imaging of the whole brain is crucial for comprehensive studies of brain structure and function. However, obtaining high quality immunofluorescence staining on cleared samples has been challenging. In this study, we developed TSA-PACT, a method combining tyramide signal amplification (TSA) and PACT, to improve sensitivity, specificity, and stability of immunofluorescence signals in the whole brain of zebrafish.
CELL AND BIOSCIENCE
(2023)
Article
Cell Biology
Omar Perbellini, Chiara Cavallini, Roberto Chignola, Marilisa Galasso, Maria T. Scupoli
Summary: This study reveals a high variability in signaling networks across different T-ALL cell lines and provides insight into the characterization of these differences using phospho-specific flow cytometry.
Article
Multidisciplinary Sciences
Ashwin Sachdeva, Claire A. Hart, Christopher D. Carey, Amy E. Vincent, Laura C. Greaves, Rakesh Heer, Pedro Oliveira, Michael D. Brown, Noel W. Clarke, Doug M. Turnbull
Summary: Advances in multiplex immunofluorescence and digital image analysis have allowed simultaneous assessment of protein defects in electron transport chain components. We developed an automated high-throughput mIF workflow for quantitative single-cell level assessment of formalin fixed paraffin embedded tissue. Using this method, we identified alterations in mitochondrial oxidative phosphorylation protein in prostate samples and observed differences in OXPHOS protein abundance.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Multidisciplinary
Mohamed Sharafeldin, Robert Hein, Jason J. Davis
Summary: We present a novel electrochemical protein quantitation method that involves shotgun biotin tagging of proteins before interfacial immunocapture and polymeric enzyme tagging. The highly amplified faradaic signals produced by a novel ferrocene-tyramine adduct allow for the detection of protein markers at attomolar levels and across a dynamic range of 5 orders of magnitude. This work supports the ultrasensitive detection of protein markers in a single antibody immunoassay format.
CHEMICAL COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
So-Hee Lim, Yun-Ju Sung, Narae Jo, Na-Yoon Lee, Kyoung-Shim Kim, Da Yong Lee, Nam-Soon Kim, Jeehun Lee, Ju-Young Byun, Yong-Beom Shin, Jae-Ran Lee
Summary: The neural circuits of the infant brain are established quickly around 6 months, but neurodevelopmental disorders are typically diagnosed at 2-3 years of age. Early diagnosis is crucial to alleviate lifelong disability, and new diagnostic methods are needed. The study investigated SCG2 serum levels as a potential biomarker for neurodevelopmental disorders and developed a highly sensitive nanoplasmonic immunosensor for early detection.
SCIENTIFIC REPORTS
(2021)
Article
Chemistry, Analytical
Guoliang Zheng, Jiangshan Dai, Haiyan Wang, Ling Li, Deyu Yuan, Shujun Bai, Xu Song, Yongyun Zhao
Summary: HNESA is a novel signal amplification technique for nucleic acid detection which overcomes the limitations of traditional methods, demonstrates high sensitivity, can distinguish mismatched sequences, and has potential applications in complex biological samples.
Article
Biochemical Research Methods
Luke T. Quigley, Lokman Pang, Elnaz Tavancheh, Matthias Ernst, Andreas Behren, Jennifer Huynh, Jessica Da Gama Duarte
Summary: This study presents a protocol for accurately identifying and characterizing tertiary lymphoid structures (TLSs) using OpalTM-tyramide signal amplification multiplex immunohistochemistry in human and murine tissue sections. The protocol allows for simultaneous detection of up to 7 markers and includes a grading system to distinguish immature and mature TLSs.
Article
Chemistry, Multidisciplinary
David E. Reynolds, Menghan Pan, Jingbo Yang, George Galanis, Yoon Ho Roh, Renee-Tyler T. Morales, Shailesh Senthil Kumar, Su-Jin Heo, Xiaowei Xu, Wei Guo, Jina Ko
Summary: Extracellular vesicles (EVs) have emerged as a promising source of biomarkers, but current diagnostic methods face challenges. A highly sensitive double digital assay is developed, allowing for absolute quantification of single molecules from individual EVs. The technology successfully separates and detects single protein molecules from single EVs. The system is applicable for evaluating important cancer biomarkers and sheds light on EV heterogeneity and discovery of new EV subtype biomarkers.
Article
Immunology
Emil Aagaard Thomsen, Sofie Andersen, Mikkel Haarslev Schroder Marqvorsen, Kristian Alsbjerg Skipper, Soren R. Paludan, Jacob Giehm Mikkelsen
Summary: This article presents a reporter system based on the expression of an unstable version of eGFP, allowing for the monitoring of individual cell activity during innate immune signaling. The system enables the detection, quantification, and isolation of cells actively producing eGFP, mimicking the production of IFN-beta. This reporter system has important applications in studying the activation and repression of the IFNB1 gene in monocytic cells and keratinocytes.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Review
Oncology
Edwin Roger Parra, Marius Ilie, Ignacio I. Wistuba, Paul Hofman
Summary: Over the past decade, there has been a revolution in cancer treatment with the shift towards targeted molecular therapies and immune-based therapies, particularly immune-checkpoint inhibitors (ICIs). However, not all patients with advanced non-small cell lung cancer (aNSCLC) benefit equally from immunotherapy, and there is a need for additional predictive markers for ICIs efficacy. Multiplex immunostaining, which evaluates multiple molecules in the tumor at the same time, shows promise in optimizing patient selection for ICIs. This review aims to explore the role of multiplex immunostaining in immuno-thoracic oncology and its current advantages and limitations in clinical practice.
BRITISH JOURNAL OF CANCER
(2023)
Article
Chemistry, Multidisciplinary
Yue Zhao, Xiaoxing Fang, Min Bai, Jin Zhang, Huahang Yu, Feng Chen, Yongxi Zhao
Summary: In this study, a microfluidic surface-enhanced Raman scattering (SERS) sensor was developed for online detection of exosomal miRNA. The sensor achieved sensitive detection of abnormal exosomal miRNA using a rolling circle amplification (RCA) and tyramine signal amplification (TSA) strategy, showing potential practical applications.
CHINESE CHEMICAL LETTERS
(2022)
Article
Chemistry, Multidisciplinary
Pengfei Zuo, Feng Gong, Yixia Yang, Xinghu Ji, Zhike He
Summary: A specific and sensitive method combining aptamer recognition and tyramide signal amplification technology was proposed for in situ fluorescence imaging of fungi. The method allows rapid observation of fungi and provides morphology and diagnostic information, making it a promising detection tool.
CHINESE CHEMICAL LETTERS
(2023)
Article
Cell Biology
One B. Dintwe, Stephen C. De Rosa, Yunda Huang, Britta S. Flach, Bryce Manso, Don Carter, Faatima Laher Omar, Katharine Schwedhelm, Chenchen Yu, Huiyin Lu, Daryl Morris, Jia Jin Kee, Valentin Voillet, Michael Stirewalt, John Hural, Zoe Moodie, Nicole Frahm, Kristen W. Cohen, M. Juliana McElrath, Erica Andersen-Nissen
Summary: This study highlights the importance of measuring vaccine immunogenicity through ICS assays. The findings revealed that the type of fetal bovine serum and the technique used to remove supernatant significantly affected the detection of vaccine antigens.
JOURNAL OF LEUKOCYTE BIOLOGY
(2022)
Article
Biochemical Research Methods
Paul H. Dannenberg, Jisoo Kang, Nicola Martino, Anokhi Kashiparekh, Sarah Forward, Jiamin Wu, Andreas C. Liapis, Jie Wang, Seok-Hyun Yun
Summary: This article demonstrates a cell barcode technology using laser particles, which can be used for cell sorting and routing through a microfluidic platform integrated with a high-speed spectrometer. By utilizing the spectral emission of laser particles, individual cells labeled with different laser colors can be distinguished and sorted.
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
Biochemical Research Methods
Sarah Black, Darci Phillips, John W. Hickey, Julia Kennedy-Darling, Vishal G. Venkataraaman, Nikolay Samusik, Yury Goltsev, Christian M. Schuerch, Garry P. Nolan
Summary: Advances in multiplexed imaging technologies, such as CODEX, using DNA-conjugated antibodies and fluorescently labeled DNA probes, allow visualization of up to 60 markers simultaneously in tissues. This enables a deep view into single-cell spatial relationships and can drive discovery in developmental biology, disease, and therapeutic design.
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.