Cytometry Part A最新文献

{"title":"Farewell Cytometry Part A","authors":"Attila Tárnok","doi":"10.1002/cyto.a.24881","DOIUrl":"10.1002/cyto.a.24881","url":null,"abstract":"<p>As I conclude my tenure as Editor-in-Chief of Cytometry Part A, I am pleased to announce that in July 2024, Professor Bartek Rajwa, a long-standing Associate Editor, will assume this role. His extensive experience and dedication make him an excellent successor, poised to lead the journal into an exciting new era. I am confident that under his stewardship, Cytometry Part A will continue to thrive as the premier publication in the field of quantitative single-cell science.</p><p>Reflecting on my journey, I am profoundly grateful for the support of my colleagues at ISAC. I especially want to thank the leadership, conference organizers, and speakers who honored me with a heartfelt farewell at the CYTO 2024 conference in Edinburgh, Scotland. Serving the cytometry community for the past 18 years has been both a privilege and a pleasure. I extend my deepest thanks to our authors and readers, whose innovative contributions and insights have been instrumental in advancing the journal.</p><p>A special note of gratitude goes to the Associate Editors, esteemed experts who have diligently upheld the highest scientific quality standards. Throughout my term, 46 colleagues have supported my efforts, some for the entire duration and others for several years. Additionally, I am indebted to the hundreds of anonymous reviewers whose dedication and critical evaluations have been crucial. The complete list of reviewers from the past 5 years can be found at the end of this issue of Cytometry Part A (add page number).</p><p>This month marks the 44th anniversary of the journal, a milestone that began with its first issue in July 1980, published by founding editor Brian H. Mayall [<span>1</span>]. During my tenure, we celebrated both the 30th [<span>2</span>] and 40th anniversaries [<span>3</span>] of the journal. As I pass the torch to Bartek Rajwa, I wish him a successful start. I am confident that Cytometry Part A, the Journal of Quantitative Single Cell Science, will continue to flourish and make significant contributions to the field for many more years.</p><p><b>Attila Tárnok:</b> Writing – original draft.</p>","PeriodicalId":11068,"journal":{"name":"Cytometry Part A","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cyto.a.24881","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141317104","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":"CPHEN-017: Comprehensive phenotyping of neutrophil extracellular traps (NETs) on peripheral human neutrophils","authors":"Ceridwyn Jones,&nbsp;Anne La Flamme,&nbsp;Peter Larsen,&nbsp;Kathryn Hally","doi":"10.1002/cyto.a.24851","DOIUrl":"10.1002/cyto.a.24851","url":null,"abstract":"<p>With the recent discovery of their ability to produce neutrophil extracellular traps (NETs), neutrophils are increasingly appreciated as active participants in infection and inflammation. NETs are characterized as large, web-like networks of DNA and proteins extruded from neutrophils, and there is considerable interest in how these structures drive disease in humans. Advancing research in this field is contingent on developing novel tools for quantifying NETosis. To this end, we have developed a 7-marker flow cytometry panel for analyzing NETosis on human peripheral neutrophils following in vitro stimulation, and in fresh circulating neutrophils under inflammatory conditions. This panel was optimized on neutrophils isolated from whole blood and analyzed fresh or in vitro stimulated with phorbol 12-myristate 13-acetate (PMA) or ionomycin, two known NET-inducing agonists. Neutrophils were identified as SSC^highFSC^highCD15⁺CD66b⁺. Neutrophils positive for amine residues and 7-Aminoactinomycin D (7-AAD), our DNA dye of choice, were deemed necrotic (Zombie-NIR⁺7-AAD⁺) and were removed from downstream analysis. Exclusion of Zombie-NIR and positivity for 7-AAD (Zombie-NIR^dim7-AAD⁺) was used here as a marker of neutrophil-appendant DNA, a key feature of NETs. The presence of two NET-associated proteins – myeloperoxidase (MPO) and neutrophil elastase (NE) – were utilized to identify neutrophil-appendant NET events (SSC^highFSC^highCD15⁺CD66b⁺Zombie NIR^dim7-AAD⁺MPO⁺NE⁺). We also demonstrate that NETotic neutrophils express citrullinated histone H3 (H3cit), are concentration-dependently induced by in vitro PMA and ionomycin stimulation but are disassembled with DNase treatment, and are present in both chronic and acute inflammation. This 7-color flow cytometry panel provides a novel tool for examining NETosis in humans.</p>","PeriodicalId":11068,"journal":{"name":"Cytometry Part A","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cyto.a.24851","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141310311","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":"Unbiased method for spectral analysis of cells with great diversity of autofluorescence spectra","authors":"Janna E. G. Roet,&nbsp;Aleksandra M. Mikula,&nbsp;Michael de Kok,&nbsp;Cora H. Chadick,&nbsp;Juan J. Garcia Vallejo,&nbsp;Henk P. Roest,&nbsp;Luc J. W. van der Laan,&nbsp;Charlotte M. de Winde,&nbsp;Reina E. Mebius","doi":"10.1002/cyto.a.24856","DOIUrl":"10.1002/cyto.a.24856","url":null,"abstract":"<p>Autofluorescence is an intrinsic feature of cells, caused by the natural emission of light by photo-excitatory molecular content, which can complicate analysis of flow cytometry data. Different cell types have different autofluorescence spectra and, even within one cell type, heterogeneity of autofluorescence spectra can be present, for example, as a consequence of activation status or metabolic changes. By using full spectrum flow cytometry, the emission spectrum of a fluorochrome is captured by a set of photo detectors across a range of wavelengths, creating an unique signature for that fluorochrome. This signature is then used to identify, or unmix, that fluorochrome's unique spectrum from a multicolor sample containing different fluorescent molecules. Importantly, this means that this technology can also be used to identify intrinsic autofluorescence signal of an unstained sample, which can be used for unmixing purposes and to separate the autofluorescence signal from the fluorophore signals. However, this only works if the sample has a singular, relatively homogeneous and bright autofluorescence spectrum. To analyze samples with heterogeneous autofluorescence spectral profiles, we setup an unbiased workflow to more quickly identify differing autofluorescence spectra present in a sample to include as “autofluorescence signatures” during the unmixing of the full stained samples. First, clusters of cells with similar autofluorescence spectra are identified by unbiased dimensional reduction and clustering of unstained cells. Then, unique autofluorescence clusters are determined and are used to improve the unmixing accuracy of the full stained sample. Independent of the intensity of the autofluorescence and immunophenotyping of cell subsets, this unbiased method allows for the identification of most of the distinct autofluorescence spectra present in a sample, leading to less confounding autofluorescence spillover and spread into extrinsic phenotyping markers. Furthermore, this method is equally useful for spectral analysis of different biological samples, including tissue cell suspensions, peripheral blood mononuclear cells, and in vitro cultures of (primary) cells.</p>","PeriodicalId":11068,"journal":{"name":"Cytometry Part A","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cyto.a.24856","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141305648","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":"Deciphering the aging process through single-cell cytometric technologies","authors":"Lok Ming Tam,&nbsp;Timothy Bushnell","doi":"10.1002/cyto.a.24852","DOIUrl":"10.1002/cyto.a.24852","url":null,"abstract":"<p>The advent of single-cell cytometric technologies, in conjunction with advances in single-cell biology, has significantly propelled forward the field of geroscience, enhancing our comprehension of the mechanisms underlying age-related diseases. Given that aging is a primary risk factor for numerous chronic health conditions, investigating the dynamic changes within the physiological landscape at the granularity of single cells is crucial for elucidating the molecular foundations of biological aging. Utilizing hallmarks of aging as a conceptual framework, we review current literature to delineate the progression of single-cell cytometric techniques and their pivotal applications in the exploration of molecular alterations associated with aging. We next discuss recent advancements in single-cell cytometry in terms of the development in instrument, software, and reagents, highlighting its promising and critical role in driving future breakthrough discoveries in aging research.</p>","PeriodicalId":11068,"journal":{"name":"Cytometry Part A","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141283242","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":"Optofluidic time-stretch imaging flow cytometry with a real-time storage rate beyond 5.9 GB/s","authors":"Dan Hou,&nbsp;Jiehua Zhou,&nbsp;Ruidong Xiao,&nbsp;Kaining Yang,&nbsp;Yan Ding,&nbsp;Du Wang,&nbsp;Guoqiang Wu,&nbsp;Cheng Lei","doi":"10.1002/cyto.a.24854","DOIUrl":"10.1002/cyto.a.24854","url":null,"abstract":"<p>Optofluidic time-stretch imaging flow cytometry (OTS-IFC) provides a suitable solution for high-precision cell analysis and high-sensitivity detection of rare cells due to its high-throughput and continuous image acquisition. However, transferring and storing continuous big data streams remains a challenge. In this study, we designed a high-speed streaming storage strategy to store OTS-IFC data in real-time, overcoming the imbalance between the fast generation speed in the data acquisition and processing subsystem and the comparatively slower storage speed in the transmission and storage subsystem. This strategy, utilizing an asynchronous buffer structure built on the producer-consumer model, optimizes memory usage for enhanced data throughput and stability. We evaluated the storage performance of the high-speed streaming storage strategy in ultra-large-scale blood cell imaging on a common commercial device. The experimental results show that it can provide a continuous data throughput of up to 5891 MB/s.</p>","PeriodicalId":11068,"journal":{"name":"Cytometry Part A","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141261036","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 5, May 2024 Cover Image","authors":"","doi":"10.1002/cyto.a.24750","DOIUrl":"10.1002/cyto.a.24750","url":null,"abstract":"","PeriodicalId":11068,"journal":{"name":"Cytometry Part A","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cyto.a.24750","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141035116","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":"Expression of Concern: Development of a 43 color panel for the characterization of conventional and unconventional T-cell subsets, B cells, NK cells, monocytes, dendritic cells, and innate lymphoid cells using spectral flow cytometry","authors":"","doi":"10.1002/cyto.a.24850","DOIUrl":"10.1002/cyto.a.24850","url":null,"abstract":"<p>\u0000 <span>Fairooz Sahir</span>, <span>Jericha Miles Mateo</span>, <span>Martin Steinhoff</span>, <span>Kodappully Sivaraman Siveen</span> (<span>2020</span>), <span>Development of a 43 color panel for the characterization of conventional and unconventional T-cell subsets, B cells, NK cells, monocytes, dendritic cells, and innate lymphoid cells using spectral flow cytometry</span>. <i>Cytometry Part A</i>, https://doi.org/10.1002/cyto.a.24288.</p><p>This Expression of Concern is for the above article, published online on 18 December 2020 in Wiley Online Library (https://onlinelibrary.wiley.com/doi/10.1002/cyto.a.24288), and has been published by agreement between the journal's Editor-in-Chief, Attila Tárnok, the International Society for Advancement of Cytometry, and Wiley Periodicals, LLC.</p><p>The Expression of Concern has been agreed due to concerns raised by the cytometry community about the validity and reproducibility of the results, and overinterpretation of the data by the authors. However, the premise of the manuscript is that a 43-color panel is possible, with the conclusion that although not optimized, it nonetheless establishes an attempt at demonstrating the possibility of analyses at this depth of dimension.</p><p>With respect to panel design and assay optimization, the authors do not provide sufficient information regarding criteria for fluorochrome selection, spillover spread characterization, unmixing control optimization, unmixing accuracy, and differences in resolution between the single stained controls and the corresponding marker in the multicolor tube. The authors mention specific metrics used for panel design without explaining their meaning or relevance. In some instances, the gating strategy was found non-standard and the positioning of the gates arbitrary. Several populations display unusual patterns compared to what is expected in normal donors, and this may result from incorrect labeling of populations, poor data quality or limited familiarity with the tools used for analysis (e.g., high percentage of cells labeled as “MAIT”, and too close proximity of monocyte and dendritic cell populations in Suppl. Fig. 1). As the settings for the algorithms used have not been provided, reproducibility and verification of the accuracy of the data proves challenging. Lastly, the discussion of the figures and supplementary data is inaccurate or overinterpreted, in particular concerning the claims of satisfactory resolution using highly overlapping dyes when comparing the fully stained sample to the single-color stained sample (Suppl. Fig. 2).</p><p>The authors were informed about the concerns raised and asked to provide an explanation. Unfortunately, the concerns have not been satisfactorily addressed by the authors in the course of the investigation. Therefore, the journal has decided to issue an Expression of Concern to inform and alert the readers.</p>","PeriodicalId":11068,"journal":{"name":"Cytometry Part A","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cyto.a.24850","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140956770","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-103: A 35-marker imaging mass cytometry panel for the co-detection of HIV and immune cell populations in human formalin fixed paraffin embedded intestinal tissue","authors":"Kevin Hu,&nbsp;Thomas O'Neil,&nbsp;Nicolas Canete,&nbsp;Heeva Baharlou,&nbsp;Andrew Harman","doi":"10.1002/cyto.a.24847","DOIUrl":"10.1002/cyto.a.24847","url":null,"abstract":"<p>We introduce a 35-marker imaging mass cytometry (IMC) panel for a detailed examination of immune cell populations and HIV RNA in formalin fixed paraffin embedded (FFPE) human intestinal tissue. The panel has broad cell type coverage and particularly excels in delineating subsets of mononuclear phagocytes and T cells. Markers for key tissue structures are included, enabling identification of epithelium, blood vessels, lymphatics, and musculature. The described method for HIV RNA detection can be generalized to other low abundance RNA targets, whether endogenous or pathogen derived. As such, the panel presented here is useful for high parameter spatial mapping of intestinal immune cells and their interactions with pathogens such as HIV.</p>","PeriodicalId":11068,"journal":{"name":"Cytometry Part A","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cyto.a.24847","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140921297","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":"Bulk lysis procedures alter target cell population counts","authors":"Laura G. Rico,&nbsp;Roser Salvia,&nbsp;Michael D. Ward,&nbsp;Jordi Petriz","doi":"10.1002/cyto.a.24848","DOIUrl":"10.1002/cyto.a.24848","url":null,"abstract":"<p>To achieve high-sensitivity cell measurements (&lt;1 in 10⁵ cells) by flow cytometry (FCM), the minimum number of acquired cells must be considered and conventional immunophenotyping protocols fall short of these numbers. The bulk lysis (BL) assay is a standardized erythrocyte lysing approach that allows the analysis of the millions of cells required for high-sensitivity measurable residual disease (MRD) detection. However, this approach has been associated with significant cell loss, along with potential over or underestimates of rare cells when using this method. The aim of this study was to evaluate bulk lysis protocols and compare them with minimal sample perturbation (MSP) protocols, which are reported to better preserve the native cellular state and avoid significant cell loss due to washing steps. To achieve this purpose, we first generated an MRD model by spiking fresh peripheral blood with K562 cells, stably expressing EGFP, at known percentages of EGFP positive cells to leukocytes. Samples were then prepared with BL and MSP protocols and analyzed using FCM. For all percentages of K562 cells established and evaluated, a significant decrease of this population was detected in BL samples compared with MSP samples, even at low K562 cell percentages. Significant decreases for non-necrotic cells were also observed in BL samples relative to MSP samples. In conclusion, the evaluation of the potential effects of BL protocols in obtaining the final count is of great interest, especially for over- or under-estimation of target cells, as in the case of measurable residual disease. Since conventional flow cytometry or minimal sample perturbation assays fall short in obtaining the minimum numbers required to reach high sensitivity measurements, significant efforts may be needed to improve bulk lysis solution reagents.</p>","PeriodicalId":11068,"journal":{"name":"Cytometry Part A","volume":null,"pages":null},"PeriodicalIF":2.5,"publicationDate":"2024-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140897615","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":"High-dimensional flow cytometry data: goldmine or fool's gold?","authors":"Paula Niewold","doi":"10.1002/cyto.a.24849","DOIUrl":"10.1002/cyto.a.24849","url":null,"abstract":"<p>Since its inception in the 1970s flow cytometry has been a valuable tool to study the characteristics of cells. Technical advancements lead to a rapid increase in the number of lasers and detectors, enabling assessment of an expanding number of parameters. As every flow cytometry user has experienced the frustration of not being able to fit all markers of interest into their panel, the prevailing mindset seemingly became the bigger the better. So, when spectral flow cytometers became commercially available, their ability to combine spectrally similar fluorophores, measure cellular autofluorescence and utilize the full light spectrum more effectively was received with enthusiasm. These attributes make spectral cytometry particularly applicable for limited or precious (clinical) material.</p><p>The recent paper from Dott et al. describes the development of a standardized protocol for sample handling, staining and acquisition, for the application of two large spectral panels in a cohort study using the ID7000™ Spectral Cell Analyzer (Sony Biotechnology).<span>¹</span> The authors specifically address the repeatability and reproducibility of staining over time, which is relevant in the context of cohort studies. By combining a 34- and 35-color spectral panel, the authors were able to quantify and identify 182 cell phenotypes in whole blood samples.</p><p>Our expanding immunological knowledge of rare and unique subsets through deep profiling has necessitated the increasing number of cellular parameters required in a single panel for accurate cell identification. However, a new set of challenges arise with increasing panel size. Although the principle of panel design and analysis remain similar, assessing data quality, defining cell populations and translating phenotypic changes into biological insight become increasingly difficult. While many papers have addressed one of these challenges, Dott et al. touch upon all three of these concerns.<span>¹</span></p><p><b>Paula Niewold:</b> Conceptualization; writing – original draft.</p>","PeriodicalId":11068,"journal":{"name":"Cytometry Part A","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cyto.a.24849","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140876133","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}