Cytometry Part A最新文献

{"title":"Size and fluorescence calibrated imaging flow cytometry: From arbitrary to standard units","authors":"Wouter W. Woud,&nbsp;Haley R. Pugsley,&nbsp;Britta A. Bettin,&nbsp;Zoltán Varga,&nbsp;Edwin van der Pol","doi":"10.1002/cyto.a.24895","DOIUrl":"10.1002/cyto.a.24895","url":null,"abstract":"<p>Imaging flow cytometry (IFCM) is a technique that can detect, size, and phenotype extracellular vesicles (EVs) at high throughput (thousands/minute) in complex biofluids without prior EV isolation. However, the generated signals are expressed in arbitrary units, which hinders data interpretation and comparison of measurement results between instruments and institutes. While fluorescence calibration can be readily achieved, calibration of side scatter (SSC) signals presents an ongoing challenge for IFCM. Here, we present an approach to relate the SSC signals to particle size for IFCM, and perform a comparability study between three different IFCMs using a plasma EV test sample (PEVTES). SSC signals for different sizes of polystyrene (PS) and hollow organosilica beads (HOBs) were acquired with a 405 nm 120 mW laser without a notch filter before detection. Mie theory was applied to relate scatter signals to particle size. Fluorescence calibration was accomplished with 2 μm phycoerythrin (PE) and allophycocyanin (APC) MESF beads. Size and fluorescence calibration was performed for three IFCMs in two laboratories. CD235a-PE and CD61-APC stained PEVTES were used as EV-containing samples. EV concentrations were compared between instruments within a size range of 100–1000 nm and a fluorescence intensity range of 3–10,000 MESF. 81 nm PS beads could be readily discerned from background based on their SSC signals. Fitting of the obtained PS bead SSC signals with Mie theory resulted in a coefficient of determination &gt;0.99 between theory and data for all three IFCMs. 216 nm HOBs were detected with all instruments, and confirmed the sensitivity to detect EVs by SSC. The lower limit of detection regarding EV-size for this study was determined to be ~100 nm for all instruments. Size and fluorescence calibration of IFCM data increased cross-instrument data comparability with the coefficient of variation decreasing from 33% to 21%. Here we demonstrate – for the first time – scatter calibration of an IFCM using the 405 nm laser. The quality of the scatter-to-diameter relation and scatter sensitivity of the IFCMs are similar to the most sensitive commercially available flow cytometers. This development will support the reliability of EV research with IFCM by providing robust standardization and reproducibility, which are pre-requisites for understanding the biological significance of EVs.</p>","PeriodicalId":11068,"journal":{"name":"Cytometry Part A","volume":"105 10","pages":"752-762"},"PeriodicalIF":2.5,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cyto.a.24895","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142139573","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":"OMIP-106: A 30-color panel for analysis of check-point inhibitory networks in the bone marrow of acute myeloid leukemia patients","authors":"Jan Musil,&nbsp;Antonin Ptacek,&nbsp;Sarka Vanikova","doi":"10.1002/cyto.a.24892","DOIUrl":"10.1002/cyto.a.24892","url":null,"abstract":"<p>Acute myeloid leukemia (AML) is the most common form of acute leukemia diagnosed in adults. Despite advances in medical care, the treatment of AML still faces many challenges, such as treatment-related toxicities, that limit the use of high-intensity chemotherapy, especially in elderly patients. Currently, various immunotherapeutic approaches, that is, CAR-T cells, BiTEs, and immune checkpoint inhibitors, are being tested in clinical trials to prolong remission and improve the overall survival of AML patients. However, early reports show only limited benefits of these interventions and only in a subset of patients, showing the need for better patient stratification based on immunological markers. We have therefore developed and optimized a 30-color panel for evaluation of effector immune cell (NK cells, γδ T cells, NKT-like T cells, and classical T cells) infiltration into the bone marrow and analysis of their phenotype with regard to their differentiation, expression of inhibitory (PD-1, TIGIT, Tim3, NKG2A) and activating receptors (DNAM-1, NKG2D). We also evaluate the immune evasive phenotype of CD33⁺ myeloid cells, CD34⁺CD38⁻, and CD34⁺CD38⁺ hematopoietic stem and progenitor cells by analyzing the expression of inhibitory ligands such as PD-L1, CD112, CD155, and CD200. Our panel can be a valuable tool for patient stratification in clinical trials and can also be used to broaden our understanding of check-point inhibitory networks in AML.</p>","PeriodicalId":11068,"journal":{"name":"Cytometry Part A","volume":"105 10","pages":"729-736"},"PeriodicalIF":2.5,"publicationDate":"2024-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cyto.a.24892","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142079625","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":"High-throughput screen to identify and optimize NOT gate receptors for cell therapy","authors":"S. Martire,&nbsp;X. Wang,&nbsp;M. McElvain,&nbsp;V. Suryawanshi,&nbsp;T. Gill,&nbsp;B. DiAndreth,&nbsp;W. Lee,&nbsp;T. P. Riley,&nbsp;H. Xu,&nbsp;C. Netirojjanakul,&nbsp;A. Kamb","doi":"10.1002/cyto.a.24893","DOIUrl":"10.1002/cyto.a.24893","url":null,"abstract":"<p>Logic-gated engineered cells are an emerging therapeutic modality that can take advantage of molecular profiles to focus medical interventions on specific tissues in the body. However, the increased complexity of these engineered systems may pose a challenge for prediction and optimization of their behavior. Here we describe the design and testing of a flow cytometry-based screening system to rapidly select functional inhibitory receptors from a pooled library of candidate constructs. In proof-of-concept experiments, this approach identifies inhibitory receptors that can operate as NOT gates when paired with activating receptors. The method may be used to generate large datasets to train machine learning models to better predict and optimize the function of logic-gated cell therapeutics.</p>","PeriodicalId":11068,"journal":{"name":"Cytometry Part A","volume":"105 10","pages":"741-751"},"PeriodicalIF":2.5,"publicationDate":"2024-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cyto.a.24893","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141995517","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":"Volume 105A, Number 8, August 2024 Cover Image","authors":"","doi":"10.1002/cyto.a.24756","DOIUrl":"https://doi.org/10.1002/cyto.a.24756","url":null,"abstract":"","PeriodicalId":11068,"journal":{"name":"Cytometry Part A","volume":"105 8","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cyto.a.24756","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141973620","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":"Evaluation of single-cell sorting accuracy using antibody-derived tag-based qPCR","authors":"Xiaoshan Shi,&nbsp;Woodrow E. Lomas III,&nbsp;Aaron Middlebrook,&nbsp;Wei Fan,&nbsp;Louise M. D'Cruz,&nbsp;Vishnu Ramani,&nbsp;Stephanie J. Widmann,&nbsp;Aaron J. Tyznik","doi":"10.1002/cyto.a.24888","DOIUrl":"10.1002/cyto.a.24888","url":null,"abstract":"<p>Single-cell sorting (index sorting) is a widely used method to isolate one cell at a time using fluorescence-activated cell sorting (FACS) for downstream applications such as single-cell sequencing or single-cell expansion. Despite widespread use, few assays are available to evaluate the proteomic features of the sorted single cell and further confirm the accuracy of single-cell sorting. With this caveat, we developed a novel assay to confirm the protein expression of sorted single cells by co-staining cells with the same marker using both antibody-derived tags (ADTs) and fluorescent antibodies. After single-cell sorting, we amplified the oligo of the ADT reagent as a surrogate signal for the protein expression using multiplex TaqMan™ qPCR on sorted cells. This assay is not only useful for confirming the identity of a sorted single cell but also an efficient method to profile proteomic features at the single-cell level. Finally, we applied this assay to characterize protein expression on whole cell lysate. Because of the sensitivity of the TaqMan™ qPCR, we can detect protein expression from a small number of cells. In summary, the ADT-based qPCR assay developed here can be utilized to confirm single-cell sorting accuracy and characterizing protein expression on both single cells and whole cell lysate.</p>","PeriodicalId":11068,"journal":{"name":"Cytometry Part A","volume":"105 10","pages":"772-785"},"PeriodicalIF":2.5,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cyto.a.24888","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141916345","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":"OMIP-105: A 30-color full-spectrum flow cytometry panel to characterize the immune cell landscape in spleen and tumor within a syngeneic MC-38 murine colon carcinoma model","authors":"Gabriel DeNiro,&nbsp;Kathryn Que,&nbsp;Trevor Fujimoto,&nbsp;Soo Min Koo,&nbsp;Bridget Schneider,&nbsp;Anandaroop Mukhopadhyay,&nbsp;Jeong Kim,&nbsp;Anandi Sawant,&nbsp;Tuan Andrew Nguyen","doi":"10.1002/cyto.a.24886","DOIUrl":"10.1002/cyto.a.24886","url":null,"abstract":"<p>This panel was designed to characterize the immune cell landscape in the mouse tumor microenvironment as well as mouse lymphoid tissues (e.g., spleen). As an example, using the MC-38 mouse syngeneic tumor model, we demonstrated that we could measure the frequency and characterize the functional status of CD4 T cells, CD8 T cells, regulatory T cells, NK cells, B cells, macrophages, granulocytes, monocytes, and dendritic cells. This panel is especially useful for understanding the immune landscape in “cold” preclinical tumor models with very low immune cell infiltration and for investigating how therapeutic treatments may modulate the immune landscape.</p>","PeriodicalId":11068,"journal":{"name":"Cytometry Part A","volume":"105 9","pages":"659-665"},"PeriodicalIF":2.5,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cyto.a.24886","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141897043","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":"Single-detector multiplex imaging flow cytometry for cancer cell classification with deep learning","authors":"Zhiwen Wang,&nbsp;Qiao Liu,&nbsp;Jie Zhou,&nbsp;Xuantao Su","doi":"10.1002/cyto.a.24890","DOIUrl":"10.1002/cyto.a.24890","url":null,"abstract":"<p>Imaging flow cytometry, which combines the advantages of flow cytometry and microscopy, has emerged as a powerful tool for cell analysis in various biomedical fields such as cancer detection. In this study, we develop multiplex imaging flow cytometry (mIFC) by employing a spatial wavelength division multiplexing technique. Our mIFC can simultaneously obtain brightfield and multi-color fluorescence images of individual cells in flow, which are excited by a metal halide lamp and measured by a single detector. Statistical analysis results of multiplex imaging experiments with resolution test lens, magnification test lens, and fluorescent microspheres validate the operation of the mIFC with good imaging channel consistency and micron-scale differentiation capabilities. A deep learning method is designed for multiplex image processing that consists of three deep learning networks (U-net, very deep super resolution, and visual geometry group 19). It is demonstrated that the cluster of differentiation 24 (CD24) imaging channel is more sensitive than the brightfield, nucleus, or cancer antigen 125 (CA125) imaging channel in classifying the three types of ovarian cell lines (IOSE80 normal cell, A2780, and OVCAR3 cancer cells). An average accuracy rate of 97.1% is achieved for the classification of these three types of cells by deep learning analysis when all four imaging channels are considered. Our single-detector mIFC is promising for the development of future imaging flow cytometers and for the automatic single-cell analysis with deep learning in various biomedical fields.</p>","PeriodicalId":11068,"journal":{"name":"Cytometry Part A","volume":"105 9","pages":"666-676"},"PeriodicalIF":2.5,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141888754","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":"Best practices for user consultation in flow cytometry shared resource laboratories","authors":"Kewal Asosingh,&nbsp;Alice Bayiyana,&nbsp;Michele C. Black,&nbsp;Uttara Chakraborty,&nbsp;Michael J. Clemente,&nbsp;Amy C. Graham,&nbsp;Michael D. Gregory,&nbsp;Karen G. Hogg,&nbsp;Gert Van Isterdael,&nbsp;ChunChun Liu,&nbsp;Lola Martínez,&nbsp;Charlotte C. Petersen,&nbsp;Ziv Porat,&nbsp;Kylie M. Price,&nbsp;Laura B. Prickett,&nbsp;Aja M. Rieger,&nbsp;Caroline E. Roe,&nbsp;Erica Smit","doi":"10.1002/cyto.a.24891","DOIUrl":"10.1002/cyto.a.24891","url":null,"abstract":"<p>This “Best Practices in User Consultation” article is the result of a 2022 International Society for the Advancement of Cytometry (ISAC) membership survey that collected valuable insights from the shared research laboratory (SRL) community and of a group discussion at the CYTO 2022 workshop of the same name. One key takeaway is the importance of initiating a consultation at the outset of a flow cytometry project, particularly for trainees. This approach enables the improvement and standardization of every step, from planning experiments to interpreting data. This proactive approach effectively mitigates experimental bias and avoids superfluous trial and error, thereby conserving valuable time and resources. In addition to guidelines, the optimal approaches for user consultation specify communication channels, methods, and critical information, thereby establishing a structure for productive correspondence between SRL and users. This framework functions as an exemplar for establishing robust and autonomous collaborative relationships. User consultation adds value by providing researchers with the necessary information to conduct reproducible flow cytometry experiments that adhere to scientific rigor. By following the steps, instructions, and strategies outlined in these best practices, an SRL can readily tailor them to its own setting, establishing a personalized workflow and formalizing user consultation services. This article provides a pragmatic guide for improving the caliber and efficacy of flow cytometry research and aggregates the flow cytometry SRL community's collective knowledge regarding user consultation.</p>","PeriodicalId":11068,"journal":{"name":"Cytometry Part A","volume":"105 9","pages":"704-712"},"PeriodicalIF":2.5,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cyto.a.24891","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141878525","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":"AutoMitoNetwork: Software for analyzing mitochondrial networks in autofluorescence images to enable label-free cell classification","authors":"Shannon Handley,&nbsp;Ayad G. Anwer,&nbsp;Aline Knab,&nbsp;Akanksha Bhargava,&nbsp;Ewa M. Goldys","doi":"10.1002/cyto.a.24889","DOIUrl":"10.1002/cyto.a.24889","url":null,"abstract":"<p>High-resolution mitochondria imaging in combination with image analysis tools have significantly advanced our understanding of cellular function in health and disease. However, most image analysis tools for mitochondrial studies have been designed to work with fluorescently labeled images only. Additionally, efforts to integrate features describing mitochondrial networks with machine learning techniques for the differentiation of cell types have been limited. Herein, we present AutoMitoNetwork software for image-based assessment of mitochondrial networks in label-free autofluorescence images using a range of interpretable morphological, intensity, and textural features. To demonstrate its utility, we characterized unstained mitochondrial networks in healthy retinal cells and in retinal cells exposed to two types of treatments: rotenone, which directly inhibited mitochondrial respiration and ATP production, and iodoacetic acid, which had a milder impact on mitochondrial networks via the inhibition of anaerobic glycolysis. For both cases, our multi-dimensional feature analysis combined with a support vector machine classifier distinguished between healthy cells and those treated with rotenone or iodoacetic acid. Subtle changes in morphological features were measured including increased fragmentation in the treated retinal cells, pointing to an association with metabolic mechanisms. AutoMitoNetwork opens new options for image-based machine learning in label-free imaging, diagnostics, and mitochondrial disease drug development.</p>","PeriodicalId":11068,"journal":{"name":"Cytometry Part A","volume":"105 9","pages":"688-703"},"PeriodicalIF":2.5,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cyto.a.24889","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141792142","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":"Volume 105A, Number 7, July 2024 Cover Image","authors":"","doi":"10.1002/cyto.a.24754","DOIUrl":"https://doi.org/10.1002/cyto.a.24754","url":null,"abstract":"","PeriodicalId":11068,"journal":{"name":"Cytometry Part A","volume":"105 7","pages":""},"PeriodicalIF":2.5,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cyto.a.24754","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141730063","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}