Cytometry Part A最新文献

{"title":"Low Dimensional Representation of Multi-Patient Flow Cytometry Datasets Using Optimal Transport for Measurable Residual Disease Detection in Leukemia.","authors":"Erell Gachon, Jérémie Bigot, Elsa Cazelles, Audrey Bidet, Jean-Philippe Vial, Pierre-Yves Dumas, Aguirre Mimoun","doi":"10.1002/cyto.a.24918","DOIUrl":"https://doi.org/10.1002/cyto.a.24918","url":null,"abstract":"<p><p>Representing and quantifying Measurable Residual Disease (MRD) in Acute Myeloid Leukemia (AML), a type of cancer that affects the blood and bone marrow, is essential in the prognosis and follow-up of AML patients. As traditional cytological analysis cannot detect leukemia cells below 5%, the analysis of flow cytometry datasets is expected to provide more reliable results. In this paper, we explore statistical learning methods based on optimal transport (OT) to achieve a relevant low-dimensional representation of multi-patient flow cytometry measurements (FCM) datasets considered as high-dimensional probability distributions. Using the framework of OT, we justify the use of the K-means algorithm for dimensionality reduction of multiple large-scale point clouds through mean measure quantization by merging all the data into a single point cloud. After this quantization step, the visualization of the intra-and inter-patient FCM variability is carried out by embedding low-dimensional quantized probability measures into a linear space using either Wasserstein Principal Component Analysis (PCA) through linearized OT or log-ratio PCA of compositional data. Using a publicly available FCM dataset and a FCM dataset from Bordeaux University Hospital, we demonstrate the benefits of our approach over the popular kernel mean embedding technique for statistical learning from multiple high-dimensional probability distributions. We also highlight the usefulness of our methodology for low-dimensional projection and clustering patient measurements according to their level of MRD in AML from FCM. In particular, our OT-based approach allows a relevant and informative two-dimensional representation of the results of the FlowSom algorithm, a state-of-the-art method for the detection of MRD in AML using multi-patient FCM.</p>","PeriodicalId":11068,"journal":{"name":"Cytometry Part A","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143540512","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A User-Centric Approach to Reliable Automated Flow Cytometry Data Analysis for Biomedical Applications.","authors":"Georg Popp, Lisa Jöckel, Michael Kläs, Thomas Wiener, Nadja Hilger, Nils Stumpf, Janek Groß, Anna Dünkel, Ulrich Blache, Stephan Fricke, Paul Franz","doi":"10.1002/cyto.a.24913","DOIUrl":"https://doi.org/10.1002/cyto.a.24913","url":null,"abstract":"<p><p>Automation and the increased number of measurable parameters in flow cytometry (FCM) have strongly increased the volume and complexity of phenotyping immune cell populations. Despite numerous automated gating methods for FCM analysis, their adoption in routine practice remains challenging due to accessibility barriers for users and potential model failures. Here, we propose a user-centered solution that combines elements of supervised machine learning (SML), rapid application development (RAD), systematic quality assurance guided by structured argumentation, and uncertainty estimation to address these challenges. We implement a data-driven model for event classification and use RAD to generate software prototypes, allowing FCM users to apply the model for automated gating. Considering concepts for structured argumentation from assurance cases (ACs), we derived and justified quality analyses that inform users about the quality of the model. We propose guiding the model operation phase using uncertainty estimation to provide users with a clear understanding of the model's confidence in its predictions. We aim to overcome barriers to the routine application of automated gating and contribute to more reliable and efficient FCM data analysis. Our approach is based on the application of phenotyping for human immune cells. We encourage future research to investigate the potential of SML, ACs, and uncertainty estimation to address dependability of data-driven models (DDMs) supporting diagnostic decision making in the medical domain, including FCM in clinical applications and highly regulated areas such as pharmaceutical research.</p>","PeriodicalId":11068,"journal":{"name":"Cytometry Part A","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143499674","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigating T-Cell Receptor Dynamics Under In Vitro Antibody-Based Stimulation Using Imaging Flow Cytometry.","authors":"Akihiro Isozaki, Kazuma Kita, Natsumi Tiffany Ishii, Yuma Oka, Maik Herbig, Mai Yamagishi, Tsubasa Wakamiya, Taketo Araki, Hiroki Matsumura, Jeffrey Harmon, Yoshitaka Shirasaki, Kangrui Huang, Yaqi Zhao, Dan Yuan, Mika Hayashi, Tianben Ding, Yuji Okamoto, Ayuko Kishimoto, Masaru Ishii, Masatoshi Yanagida, Keisuke Goda","doi":"10.1002/cyto.a.24916","DOIUrl":"https://doi.org/10.1002/cyto.a.24916","url":null,"abstract":"<p><p>T cells play a pivotal role in the immune system's response to various conditions. They are activated by antigen-presenting cells (APCs) via T-cell surface receptors, resulting in cytokine production and T-cell proliferation. These interactions occur through the formation of immunological synapses. The advent of imaging flow cytometry has enabled detailed statistical analyses of these cellular interactions. However, the dynamics of T-cell receptors in response to in vitro stimulation are yet to receive attention, despite it being a crucial aspect of understanding T-cell behavior. In this article, we explore the responses of T cells to in vitro antibody-based stimulation without APCs. Specifically, we established a Th1 cell clone, subjected it to a combination of centrifugation-induced mechanical stress and anti-human CD3 and anti-human CD28 antibody stimulation as the in vitro antibody-based stimulation, and captured and analyzed bright-field and fluorescence images of single cells various hours after stimulation using an imaging flow cytometer. Our results indicate distinct temporal dynamics of CD3 and CD28. Notably, CD3 and CD28 relocated on the T-cell surface immediately after stimulation, with CD3 receptors dispersing after 3.5 h, whereas CD28 remained clustered for 7.5 h. These receptor morphological changes precede cytokine production, suggesting their potential as early indicators of T-cell activation.</p>","PeriodicalId":11068,"journal":{"name":"Cytometry Part A","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143467300","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantifying Nuclear Structures of Digital Pathology Images Across Cancers Using Transport-Based Morphometry.","authors":"Mohammad Shifat-E-Rabbi, Natasha Ironside, Naqib Sad Pathan, John A Ozolek, Rajendra Singh, Liron Pantanowitz, Gustavo K Rohde","doi":"10.1002/cyto.a.24917","DOIUrl":"10.1002/cyto.a.24917","url":null,"abstract":"<p><p>Alterations in nuclear morphology are useful adjuncts and even diagnostic tools used by pathologists in the diagnosis and grading of many tumors, particularly malignant tumors. Large datasets such as TCGA and the Human Protein Atlas, in combination with emerging machine learning and statistical modeling methods, such as feature extraction and deep learning techniques, can be used to extract meaningful knowledge from images of nuclei, particularly from cancerous tumors. Here, we describe a new technique based on the mathematics of optimal transport for modeling the information content related to nuclear chromatin structure directly from imaging data. In contrast to other techniques, our method represents the entire information content of each nucleus relative to a template nucleus using a transport-based morphometry (TBM) framework. We demonstrate that the model is robust to different staining patterns and imaging protocols, and can be used to discover meaningful and interpretable information within and across datasets and cancer types. In particular, we demonstrate morphological differences capable of distinguishing nuclear features along the spectrum from benign to malignant categories of tumors across different cancer tissue types, including tumors derived from liver parenchyma, thyroid gland, lung mesothelium, and skin epithelium. We believe these proof-of-concept calculations demonstrate that the TBM framework can provide the quantitative measurements necessary for performing meaningful comparisons across a wide range of datasets and cancer types that can potentially enable numerous cancer studies, technologies, and clinical applications and help elevate the role of nuclear morphometry into a more quantitative science.</p>","PeriodicalId":11068,"journal":{"name":"Cytometry Part A","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143467302","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CytoNorm 2.0: A flexible normalization framework for cytometry data without requiring dedicated controls.","authors":"Katrien L A Quintelier, Marcella Willemsen, Victor Bosteels, Joachim G J V Aerts, Yvan Saeys, Sofie Van Gassen","doi":"10.1002/cyto.a.24910","DOIUrl":"https://doi.org/10.1002/cyto.a.24910","url":null,"abstract":"<p><p>Cytometry is a single cell, high-dimensional, high-throughput technique that is being applied across a range of disciplines. However, many elements alongside the data acquisition process might give rise to technical variation in the dataset, called batch effects. CytoNorm is a normalization algorithm for batch effect removal in cytometry data that was originally published in 2020 and has been applied on a variety of datasets since then. Here, we present CytoNorm 2.0, discussing new, illustrative use cases to increase the applicability of the algorithm and showcasing new visualizations that enable thorough quality control and understanding of the normalization process. We explain how CytoNorm can be used without the need for technical replicates or controls, show how the goal distribution can be tailored toward the experimental design and we elaborate on the choice of markers for CytoNorm's internal FlowSOM clustering step.</p>","PeriodicalId":11068,"journal":{"name":"Cytometry Part A","volume":" ","pages":""},"PeriodicalIF":2.5,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143051951","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"OMIP-110: A 37-Color Spectral Flow Cytometric Panel to Assess Transcription Factors and Chemokine Receptors in Human Intestinal Lymphoid Cells","authors":"Qinyue Jiang,&nbsp;Ciska Lindelauf,&nbsp;Vincent van Unen,&nbsp;Andrea E. van der Meulen-de Jong,&nbsp;Frits Koning,&nbsp;M. Fernanda Pascutti","doi":"10.1002/cyto.a.24914","DOIUrl":"10.1002/cyto.a.24914","url":null,"abstract":"<p>We have developed a 37-color spectral flow cytometry panel to assess the phenotypical differentiation of innate and adaptive immune lymphoid subsets within human intestinal tissue. In addition to lineage markers for identifying innate lymphoid cells (ILC), TCRγδ, MAIT (mucosal-associated invariant T), natural killer (NK), CD4⁺ and CD8⁺ T cells, we incorporated markers of differentiation and activation (CD45RA, CD45RO, CD25, CD27, CD38, CD39, CD69, CD103, CD127, CD161, HLA-DR, CTLA-4 [CD152]), alongside transcription factors (Bcl-6, FoxP3, GATA-3, Helios, T-bet, PU.1 and RORγt) and chemokine receptors (CCR4, CCR6, CCR7, CXCR3, and CXCR5). Additionally, Granzyme B and Ki-67 were included to assess cytotoxicity and proliferation potential of the different subsets. This panel is currently used for in-depth immunophenotyping in endoscopic biopsies and peripheral blood mononuclear cells (PBMC) from inflammatory bowel disease (IBD) patients. Distinguished from other OMIP papers, the comprehensive detection of both transcription factors and chemokine receptors facilitates the efficient assessment of several subsets, particularly CD4⁺ T helper cells, and its potential application extends to both tissue and circulation.</p>","PeriodicalId":11068,"journal":{"name":"Cytometry Part A","volume":"107 1","pages":"9-35"},"PeriodicalIF":2.5,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cyto.a.24914","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143001752","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Measuring the size of oil droplets in a flow cytometer using Mie resonances: A possible size calibration ladder for 0.5–6 μm","authors":"Richard E. Cavicchi,&nbsp;Dean C. Ripple,&nbsp;Joshua A. Welsh,&nbsp;Jerilyn R. Izac,&nbsp;Alexander W. Peterson,&nbsp;Aaron M. Goldfain,&nbsp;Wyatt N. Vreeland","doi":"10.1002/cyto.a.24912","DOIUrl":"10.1002/cyto.a.24912","url":null,"abstract":"<p>An emulsion of silicone oil droplets in aqueous buffer produces a distinctive series of peaks or resonances in the side scatter histogram in a flow cytometer. As many as 12 peaks are observed in the violet-side scatter channel at 405 nm, with half that number observed in the blue side scatter channel at 488 nm. Using the index of refraction of the oil and buffer, the wavelength of light, and the collection angle and gain of the instrument, we assign the peaks to specific diameters at which Mie resonances occur. With the close match for the index of refraction of silicone oil (<i>n</i> = 1.417 at 405 nm) to biological materials, these resonances could form the basis of a finely spaced size calibration ladder in the range 0.5–6 μm for estimating the size of biological particles in a flow cytometer. Resonances were also observed using mineral oil (<i>n</i> = 1.483 at 405 nm) suggesting that investigating and modeling resonances for emulsion systems may be useful for understanding these systems.</p>","PeriodicalId":11068,"journal":{"name":"Cytometry Part A","volume":"107 1","pages":"45-53"},"PeriodicalIF":2.5,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cyto.a.24912","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143001754","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ultrastructural Remodeling of Cardiomyocytes in Postinfarction Myocardium of Rats in the Late Stages of the Disease","authors":"Sergei A. Fedotov,&nbsp;Andrei V. Stepanov,&nbsp;Galina A. Sakuta,&nbsp;Ivan S. Andreev,&nbsp;Marina S. Ivanova,&nbsp;Ekaterina V. Baidyuk","doi":"10.1002/cyto.a.24915","DOIUrl":"10.1002/cyto.a.24915","url":null,"abstract":"<div>\u0000 \u0000 <p>Identifying factors that contribute to the transition to the dilated phase in cardiac ischemia is a critical challenge in heart failure treatment. Currently, no effective therapies exist for this ischemic complication, and the mechanisms driving left ventricular dilatation during chronic post-infarction remodeling remain poorly understood. One potential pathological process leading to ventricular dilatation involves specific compensatory rearrangements in the border zone adjacent to the infarct, which isolates the intact myocardium from inflammation at the scar edge. Using a rat model, we examined ultrastructural changes in the intact and border zones of post-infarction myocardium at chronic stages. Morphometric analysis of myofibrils, mitochondria, and excitation-contraction coupling structures revealed similar remodeling processes in both zones at 2 weeks post-infarction, characterized by decreased myofibril density, reduced mitochondrial area and volume density, and shortened contacts between T-tubules and sarcoplasmic reticulum. At 26 weeks post-infarction, during the dilated cardiomyopathy phase, we observed distinct compensatory changes in the border zone. Specifically, there was a loose arrangement of myofibrils and an increased volume fraction of mitochondria. These differences in remodeling between the intact and border zones highlight factors contributing to ventricular dilatation and help the development of new therapeutic strategies to delay heart failure progression in cardiac ischemia.</p>\u0000 </div>","PeriodicalId":11068,"journal":{"name":"Cytometry Part A","volume":"107 1","pages":"36-44"},"PeriodicalIF":2.5,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142909423","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Volume 105A, Number 12, December 2024 Cover Image","authors":"","doi":"10.1002/cyto.a.24764","DOIUrl":"https://doi.org/10.1002/cyto.a.24764","url":null,"abstract":"","PeriodicalId":11068,"journal":{"name":"Cytometry Part A","volume":"105 12","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cyto.a.24764","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142861233","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Autofluorescence lifetime flow cytometry rapidly flows from strength to strength","authors":"Klaus Suhling","doi":"10.1002/cyto.a.24909","DOIUrl":"10.1002/cyto.a.24909","url":null,"abstract":"&lt;p&gt;[Color figure can be viewed at wileyonlinelibrary.com]&lt;/p&gt;&lt;p&gt;In flow cytometry, the fluorescence lifetime of the reduced form of co-enzymes nicotinamide dinucleotide (NADH) and nicotinamide dinucleotide phosphate (NADPH) can be used as a reporter of metabolic activity in single cells. Moreover, their metabolic state can be determined faster than imaging them with fluorescence lifetime imaging (FLIM), as reported by Samimi et al. [&lt;span&gt;1&lt;/span&gt;].&lt;/p&gt;&lt;p&gt;Ever since Britton Chance highlighted the benefits of using autofluorescence of cells to study metabolism, respiration and associated redox reactions in cells and tissues in the 1960s, [&lt;span&gt;2&lt;/span&gt;] this topic has attracted the attention the biophysics, biochemistry and life science research communities [&lt;span&gt;3&lt;/span&gt;]. FLIM is now routinely used to study NADH and NADPH fluorescence lifetimes, but here the authors show that not only no fluorescence labelling is required but imaging can also be dispensed with.&lt;/p&gt;&lt;p&gt;Autofluorescence is the term given to the fluorescence from naturally occurring fluorophores in cells or tissue without adding any exogenous fluorophores or labels—the fluorescence originates from intrinsic fluorophores. There is a whole range of biological intrinsic fluorophores, such as some amino acids, flavins, lipofuscin, chlorophyll, porphyrins, carotenoids, collagen, elastin and others that fluoresce naturally when excited with light of an appropriate wavelength [&lt;span&gt;4, 5&lt;/span&gt;]. While fluorescence of some amino acids can be excited around 280 nm, where glass is opaque, the autofluorescence of NADH and NADPH has an absorption peak around 350 nm and can conveniently be excited at 375 nm—a wavelength at which glass is transparent [&lt;span&gt;6&lt;/span&gt;]. This is a big advantage facilitating uptake of this approach by the scientific community, especially considering the ubiquitous use of glass in the life sciences.&lt;/p&gt;&lt;p&gt;NADH and NADPH are pyridine nucleotides and the fluorescence originates from their nicotinamide ring, peaking at around 460 nm or so [&lt;span&gt;7&lt;/span&gt;]. They are small molecules that play a big role in redox reactions, respiration and metabolism, and allow the optical investigation, via their fluorescence, of biochemical states and metabolic pathways in cells and tissues [&lt;span&gt;3&lt;/span&gt;].&lt;/p&gt;&lt;p&gt;In general, fluorescence can be characterized by several features: intensity, wavelength, lifetime and polarization, and, in combination with microscopy, the position in the image where it originates from. The more of these parameters can be measured, the higher the biochemical resolving power of the measurement [&lt;span&gt;8&lt;/span&gt;]. The fluorescence intensity can yield information about location, concentration and fluorescence quantum yield, the spectrum about the color of the emission (e.g., used to highlighting neurons in different colors in “brainbow” samples in neuroscience [&lt;span&gt;9&lt;/span&gt;]), the lifetime about the time the fluorophores resides in the excited state (typicall","PeriodicalId":11068,"journal":{"name":"Cytometry Part A","volume":"107 1","pages":"5-8"},"PeriodicalIF":2.5,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cyto.a.24909","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142767366","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}