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The immune cellular landscape from the gastric mucosa remains largely unknown despite its relevance in several inflammatory conditions. Human gastric biopsies were obtained from the antrum, body and incisura from 10 individuals to obtain lamina propria mononuclear cells that were further characterized by spectral cytometry. Phenotypic hierarchical analyses identified a total of 52 different immune cell subsets within the human gastric mucosa revealing that T-cells (> 60%) and NK cells (> 20%) were the main populations. Within T-cells, CD4 + and CD8 + were equally represented with both subsets displaying mainly a memory and effector phenotype. NK cells, on the contrary, were largely of the early phenotype. No regional differences were observed for any subsets among the 3 locations. Following unsupervised analysis, a total of 82 clusters were found. Again, no differences were observed amongst locations although a great degree of inter-individual variability was found, largely influenced by the presence of H. pylori infection and dyspepsia. We have unraveled the human gastric immune cellular subset composition and a unique interindividual immune fingerprint with no inter-regional variations., Competing Interests: Declarations Competing interests The authors declare no competing interests., (© 2024. The Author(s).)

Single-cell cytometry data are crucial for understanding the role of the immune system in diseases and responses to treatment. However, traditional methods for annotating cytometry data face challenges in scalability, robustness, and accuracy. We propose a cytometry masked autoencoder (cyMAE), which automates immunophenotyping tasks including cell type annotation. The model upholds user-defined cell type definitions, facilitating interpretability and cross-study comparisons. The training of cyMAE has a self-supervised phase, which leverages large amounts of unlabeled data, followed by fine-tuning on specialized tasks using smaller amounts of annotated data. The cost of training a new model is amortized over repeated inferences on new datasets using the same panel. Through validation across multiple studies using the same panel, we demonstrate that cyMAE delivers accurate and interpretable cellular immunophenotyping and improves the prediction of subject-level metadata. This proof of concept marks a significant step forward for large-scale immunology studies., Competing Interests: Declaration of interests E.J.W. is a member of the Parker Institute for Cancer Immunotherapy, which supports cancer immunotherapy research in his laboratory. E.J.W. is an advisor for Arsenal Biosciences, Coherus, Danger Bio, IpiNovyx, NewLimit, Marengo, Pluto Immunotherapeutics, Related Sciences, Santa Ana Bio, and Synthekine. E.J.W. is a founder of and holds stock in Coherus, Danger Bio, Prox Biosciences, and Arsenal Biosciences., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Despite remarkable improvements in the survival of pediatric acute lymphoblastic leukemia (ALL), sensitive detection and clinical management of central nervous system leukemia (CNSL) are still immensely challenging. Blast cells residing in the CNS but not circulating in the cerebrospinal fluid (CSF) remain undetected by current diagnostic methods, preventing a truly risk-adapted anti-leukemic treatment in this compartment. We examined the clinical applicability of the molecular marker microRNA (miR)-181a quantified in the cell-free CSF to evaluate the level of CNS involvement and to optimize patient stratification based on CNS status. Normalized copy number of miR-181a was longitudinally profiled using droplet digital PCR, and the results were compared with the degree of leukemic involvement of the CNS. After combining cytospin- and flow cytometry (FCM) data with miR-181a expression, we could stratify previously ambiguous cases and reclassify patients into a CNS-positive/miR-significant group (mean ± SE for miR-181a copies: 3300.70 ± 809.69) bearing remarkable infiltration as well as into CNS-minimal/miR-significant and CNS-minimal/miR-minimal groups differentiating putative, clinically significant occult CNSL cases (2503.50 ± 275.89 and 744.02 ± 86.81 copies, respectively, p = 1.13 × 10 -6 ). In summary, miR-181a expression is a promising biomarker for CNSL detection, facilitating the robust identification of patients who could benefit from intensified CNS-directed therapy., Competing Interests: Ethics approval and consent to participate All procedures performed in this study, involving human participants were in accordance with the ethical standards of the Medical Research Council of Hungary, and with the 1964 Helsinki declaration and its later amendments. The study was approved by the central ethical committee (institute: National Scientific and Ethical Committee of the Medical Research Council of Hungary (ETT-TUKEB), approval numbers: 60106–1/2015/EKU and 6886/2019/EKU). The study is compliant with all relevant ethical regulations for human research participants, and informed consent was obtained from all patients or legal guardians. Consent for publication The study is compliant with all relevant ethical regulations for human research participants, and informed consent was obtained from all patients or legal guardians. Data availability The original contributions presented in the study are included in the article, further inquiries can be directed to the corresponding author. Competing interests The authors declare no competing interests., (© 2024. The Author(s).)

The lung immune system consists of both resident and circulating immune cells that communicate intricately. The immune system is activated by exposure to bacteria and viruses, when cancer initiates in the lung (primary lung cancer), or when metastases of other cancer types, including breast cancer, spread to and develop in the lung (secondary lung cancer). Thus, in these pathological situations, a comprehensive and quantitative assessment of changes in the lung immune system is of paramount importance for understanding mechanisms of infectious diseases, lung cancer, and metastasis but also for developing efficacious treatments. Unfortunately, lung tissue exhibits high autofluorescence, and this high background signal makes high-parameter flow cytometry analysis complicated. Here, we provide an optimized 30-parameter antibody panel for the analysis of all major immune cell types and states in normal and metastatic murine lungs using spectral flow cytometry., Competing Interests: Declaration of interests C.W. is a current employee of BioLegend, Inc., (Copyright © 2024 University of Basel, Department of Biomedicine. Published by Elsevier Inc. All rights reserved.)

The cell cycle is a fundamental process essential for cell proliferation, differentiation and development. It consists of four major phases: G1, S, G2 and M. These phases collectively drive the reproductive cycle and are meticulously regulated by various proteins that play crucial roles in both the prevention and progression of cancer. Traditional methods for studying these functions, such as flow cytometry, require a substantial number of cells to ensure accuracy. In this study, we have developed a user-friendly immunofluorescence-based method for identifying cell cycle stages, providing single-cell resolution and precise identification of G1, early/mid S, late S, early/mid G2, late G2, and each sub-stage of the M phase using fluorescence microscopy called ImmunoCellCycle-ID. This method provides high-precision cell cycle identification and can serve as an alternative to, or in combination with, traditional flow cytometry to dissect detailed sub-stages of the cell cycle in a variety of cell lines., Competing Interests: Competing interests The authors declare no competing or financial interests., (© 2024. Published by The Company of Biologists Ltd.)

Flow cytometry enables quantitative measurements of fluorescence in single cells. The technique was widely used for immunology to identify populations with different surface protein markers. More recently, the usage of flow cytometry has been extended to additional readouts, including intracellular proteins and fluorescent protein transgenes, and is widely utilized to study developmental biology, systems biology, microbiology, and many other fields. A common file format (FCS format, defined by the International Society for Advancement of Cytometry (ISAC)) has been universally adopted, facilitating data exchange between different machines. A diverse spectrum of software packages has been developed for the analysis of flow cytometry data. However, those are either 1) costly proprietary softwares, 2) open source packages with prerequisite installation of R or Python and sometimes require users to have experience in coding, or 3) online tools that are limiting for analysis of large data sets. Here, we present EasyFlow, an open-source flow cytometry analysis graphic user interface (GUI) based on Matlab or Python, that can be installed and run locally across platforms (Windows, MacOS, and Linux) without requiring previous coding knowledge. The Python version (EasyFlowQ) is also developed on a popular plotting framework (Matplotlib) and modern user interface toolkit (Qt), allowing more advanced users to customize and keep contributing to the software, as well as its tutorials. Overall, EasyFlow serves as a simple-to-use tool for inexperienced users with little coding experience to use locally, as well as a platform for advanced users to further customize for their own needs., Competing Interests: Y.E.A. is a scientific advisory board member and consultant at TeraCyte. There are no patents, products in development or marketed products associated with this research to declare. This does not alter our adherence to PLOS ONE policies on sharing data and materials., (Copyright: © 2024 Ma et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Cellular phenotype and function are altered in different microenvironments. For targeted therapies it is important to understand site-specific cellular adaptations. Juvenile idiopathic arthritis (JIA) is characterized by autoimmune joint inflammation, with frequent inadequate treatment responses. To comprehensively assess the inflammatory immune landscape, we designed a 37-parameter spectral flow cytometry panel delineating mononuclear cells from JIA synovial fluid (SF) of autoimmune inflamed joints, compared to JIA and healthy control blood. Synovial monocytes and NK cells (CD56bright) lack Fc-receptor CD16, suggesting antibody-mediated targeting may be ineffective. B cells and DCs, both in small frequencies in SF, undergo maturation with high 4-1BB, CD71, CD39 expression, supporting T-cell activation. SF effector and regulatory T cells were highly active with newly described co-receptor combinations that may alter function, and suggestion of metabolic reprogramming via CD71, TNFR2, and PD-1. Most SF effector phenotypes, as well as an identified CD4-Foxp3+ T-cell population, were restricted to the inflamed joint, yet specific SF-predominant CD4+ Foxp3+ Treg subpopulations were increased in blood of active but not inactive JIA, suggesting possible recirculation and loss of immunoregulation at distal sites. This first comprehensive dataset of the site-specific inflammatory landscape at protein level will inform functional studies and the development of targeted therapeutics to restore immunoregulatory balance and achieve remission in JIA., (© The Author(s) 2024. Published by Oxford University Press on behalf of the British Society for Immunology.)

Research on central nervous system tumors (CNSTs) has a significant impact on the diagnosis and prognosis of patients. Currently, CNSTs are classified according to the schema proposed by the World Health Organization (WHO), which considers clinical, histopathological, and molecular characteristics, highlighting the importance of tumor biology for accurate diagnosis and optimal treatment approaches. Despite these advances, assessing DNA ploidy-a marker of tumor aggressiveness-remains complex in CNSTs. This review investigates the utility of DNA index (DNAi) and DNA ploidy analysis by flow cytometry in diagnosing CNSTs and prognosing their outcomes. We systematically reviewed studies in the PubMed database from 1990 to the present using the keywords "DNA Index", "Brain", "Flow cytometry", and "Ploidy". We identified 151 studies, 36 of which met our inclusion criteria. We found considerable variation in sample sizes and methodological variation across the studies. Discrepancies between the reported DNAi and ploidy values were observed. Aneuploidy is generally associated with more aggressive tumors, although exceptions exist. Higher DNAi levels correlate with increased malignancy, notably in glioblastomas, astrocytomas, and meningiomas, whereas diploid astrocytomas and oligodendrogliomas are associated with shorter survival rates. DNA ploidy assessment via flow cytometry could predict CNST behavior, yet methodological issues with tissue selection, adequate control samples, and technique variability remain. DNAi and ploidy assessments show promise as prognostic markers in CNSTs. However, the standardization of flow cytometry protocols and alignment with the current WHO classification schema are essential steps to integrate ploidy analysis in routine CNST assessment., Competing Interests: Declarations Ethical approval Not applicable. Competing interests The authors declare no competing interests., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

Flow cytometry (FCM) is used to detect lymphocyte subsets and evaluate the level of cellular immunity in the body, which is one of the commonly used FCM detection projects in clinical practice. To date, numerous institutions and academic organizations, both domestically and internationally, have published guidelines and consensus documents covering various aspects, including the establishment of cytometry laboratories, standardized procedures for detecting lymphocyte subsets, and their clinical applications across different fields, each with a distinct focus. However, in clinical practice, laboratories continue to face challenges in establishing standardized quality management systems, implementing quality assurance activities, developing appropriate detection protocols and gating strategies for various scenarios, and identifying and resolving common issues encountered during detecting. Currently, there is no unified consensus on these issues. To standardize the development of quality management systems for lymphocyte subsets detecion via FCM, enhance laboratory quality management practices, and ensure the accuracy and reliability of results, the Laboratory Medicine Committee of Chinese Association of Integrative Medicine (LMC-CAIM) convened experts to formulate this expert consensus.

Bay-scale empirical evaluations of how bivalve aquaculture alters plankton composition, and subsequently ecological functioning and higher trophic levels, are lacking. Temporal, inter- and within-bay variation in hydrodynamic, environmental, and aquaculture pressure complicate plankton monitoring design to detect bay-scale changes and inform aquaculture ecosystem interactions. Here, we used flow cytometry to investigate spatio-temporal variations in bacteria and phytoplankton (< 20 μm) composition in four bivalve aquaculture embayments. We observed higher abundances of bacteria and phytoplankton in shallow embayments that experienced greater freshwater and nutrient inputs. Depleted nutrient conditions may have led to the dominance of picophytoplankton cells, which showed strong within-bay variation as a function of riverine vs marine influence and nutrient availability. Although environmental forcings appeared to be a strong driver of spatio-temporal trends, results showed that bivalve aquaculture may reduce near-lease phytoplankton abundance and favor bacterial growth. We discuss confounding environmental factors that must be accounted for when interpreting aquaculture effects such as grazing, benthic-pelagic coupling processes, and microbial biogeochemical cycling. Conclusions provide guidance on sampling considerations using flow cytometry in aquaculture sites based on embayment geomorphology and hydrodynamics., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Sharpe et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The microfluidic impedance flow cytometer (m-IFC) using constricted microchannels is an appealing choice for the high-throughput measurement of single-cell mechanical properties. However, channels smaller than the cells are susceptible to irreversible blockage, extremely affecting the stability of the system and the throughput. Meanwhile, the common practice of extracting a single quantitative index, i.e., total cell passage time, through the constricted part is inadequate to decipher the complex mechanical properties of individual cells. Herein, this study presents a long-term stable and multifeature m-IFC based on a constricted channel for single-cell mechanical phenotyping. The blockage problem is effectively overcome by adding tiny xanthan gum (XG) polymers. The cells can pass through the constricted channel at a flow rate of 500 μL/h without clogging, exhibiting high throughput (∼240 samples per second) and long-term stability (∼2 h). Moreover, six detection regions were implemented to capture the multiple features related to the whole process of a single cell passing through the long-constricted channel, e.g., creep, friction, and relaxation stages. To verify the performance of the multifeature m-IFC, cells treated with perturbations of microtubules and microfilaments within the cytoskeleton were detected, respectively. It suggests that the extracted features provide more comprehensive clues for single-cell analysis in structural and mechanical transformation. Overall, our proposed multifeature m-IFC exhibits the advantages of nonclogging and high throughput, which can be extended to other cell types for nondestructive and real-time mechanical phenotyping in cost-effective applications.

Background: Immune dysregulation is a hallmark of autoimmune diseases of the central nervous system (CNS), characterized by an excessive immune response, and primary CNS tumors (pCNS-tumors) showing a highly immunosuppressive parenchymal microenvironment., Methods: Aiming to provide novel insights into the pathogenesis of CNS autoimmunity and cerebral tumor immunity, we analyzed the peripheral blood (PB) and cerebrospinal fluid (CSF) of 81 autoimmune limbic encephalitis (ALE), 148 relapsing-remitting multiple sclerosis (RRMS), 33 IDH-wildtype glioma, 9 primary diffuse large B cell lymphoma of the CNS (CNS-DLBCL), and 110 controls by flow cytometry (FC). Additionally, an in-depth immunophenotyping of the PB from an independent cohort of 20 RRMS and 18 IDH-wildtype glioblastoma patients compared to 19 controls was performed by FC combined with unsupervised computational approaches., Results: We identified alterations in peripheral and intrathecal adaptive immunity, mainly affecting the T cell (Tc) but also the B cell (Bc) compartment in ALE, RRMS, and pCNS-tumors compared to controls. ALE, RRMS, and pCNS-tumors featured higher expression of the T cell activation marker HLA-DR, which was even more pronounced in pCNS-tumors than in ALE or RRMS. Glioblastoma patients showed signs of T cell exhaustion that were not visible in RRMS patients. In-depth characterization of the PB revealed differences mainly in the T effector and memory compartment between RRMS and glioblastoma patients and similar alterations in the Bc compartment, including atypical Bc, CD19 + CD20 - double negative Bc, and plasma cells. PB and CSF mFC together with CSF routine parameters could reliably differentiate ALE and RRMS from pCNS-tumors facilitating early diagnosis and treatment., Conclusions: ALE, RRMS, and pCNS-tumors show distinct but partially overlapping changes mainly in HLA-DR + Tc, memory Tc, exhausted Tc, and Bc subsets providing insights into disease pathogenesis. Moreover, mFC shows diagnostic potential facilitating early diagnosis and treatment., (© 2024. The Author(s).)

Background: Single-platform flow cytometry technology together with CD45-gating is becoming the method of choice for absolute CD4 T cell enumeration. Immunological assessment of HIV patients by monitoring CD4 can provide valuable information on antiviral treatment response and disease progression., Methods: A total of 97 HIV-positive individuals were recruited from 2 hospitals in Tripoli, Libya, and 14 healthy blood donors. The HIV-infected individuals were classified by CD4+ count into HIV-positive (>200 cells/µL) or AIDS (≤200 cells/µL) groups. CD4+ and CD8+ cell counts were determined and compared among the groups and with similar published data., Results: The mean ± SD CD4+ cell counts were 1106 ± 442.8 cells/µL in healthy individuals, 460 ± 219.7 cells/µL in the HIV-positive group, and 78 ± 64.3 cells/µL in the AIDS group. The mean ± SD CD4+/CD8+ ratio was 1.6 ± 0.58, 0.4 ± 0.22, and 0.1 ± 0.1, respectively. CD4+ counts in Libyan healthy adults might be higher than those reported in several studies in other regions, whereas CD4+ counts in Libyan AIDS patients seem lower., Conclusion: Reference values for T lymphocyte counts in Libyan healthy individuals should be investigated more extensively, and the reasons why Libyan AIDS patients seem to have such lower CD4+ counts should be examined., (© The Author(s) 2024. Published by Oxford University Press on behalf of American Society for Clinical Pathology. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Purpose: The present study explores the dynamics of cell death in Hirschsprung's disease (HSCR) and control (CO) groups under inflammatory stress conditions., Methods: Using flow cytometry, we analyzed intestinal colonic organoid cultures derived from the ganglionic segment of the HSCR and CO groups. Our analysis focused on the quantification of RIPK1-independent and RIPK1-dependent apoptosis, as well as necroptosis in both viable and non-viable cells under acute and chronic inflammatory stress., Results: Our findings indicate that HSCR cells are particularly vulnerable to inflammation during acute proinflammatory stress, as evidenced by an increase in dead cells (Zombie +). Under chronic conditions, adaptive changes are observed in both HSCR and CO groups, indicating survival mechanisms. These adaptations are uniquely altered in HSCR, suggesting an impaired response to chronic inflammation. HSCR cells show significantly decreased RIPK1-dependent apoptosis in acute scenarios compared to chronic ones, unlike the CO group, implying varied responses to different inflammatory stresses. In non-viable cells, considerable changes in RIPK1-dependent apoptosis under chronic conditions in HSCR indicate a heightened inflammatory response compared to CO., Conclusion: This research provides insights into cell death regulation in HSCR under inflammatory stress by using patient-derived organoids, underscoring the complexity of its inflammatory response., (© 2024. The Author(s).)

Background: Researching medical sample storage is crucial for maintaining the integrity of biological specimens and ensuring the accuracy of research investigations and diagnostic tests. Improper storage conditions can lead to sample degradation, compromising the reliability of results. Standardized storage procedures are essential for quality control, particularly in multicenter trials where samples are collected and processed at various locations. Moreover, ethical considerations dictate careful handling of patient samples to uphold privacy and rights., Methods: This study focuses on the surface phenotype of T cells, which is vital for diagnosing immunodeficiency disorders and autoimmune diseases and for monitoring disease activity and treatment efficacy. The effect of storage duration on T cell surface proteins is multifactorial, influenced by factors like protein degradation, cellular metabolism, and cytokine release. Long-term storage can lead to the gradual loss of T cell function, necessitating techniques to preserve cell activity. Changes in surface markers can affect disease diagnosis, emphasizing the importance of accurate sample processing., Results: Findings from this study reveal time-dependent changes in T cell surface markers during storage. CD3 levels declined significantly after the fourth day, with FITC labeling proving superior to APC. CD4 levels remained consistent until the fourth day, contrasting with previous findings on foreskin tissue. HLA-DR levels declined rapidly, indicating unsuitability for storage, consistent with other studies on cryopreserved cells. CD16 and CD8 levels decreased gradually, while CD56 declined rapidly after the third day, consistent with recent research., Conclusions: There were detectable and significant differences after the samples were stored for an improper period, which may have affected the integrity of the results, suggesting that understanding the factors influencing T cell surface protein changes during storage is crucial for maintaining result integrity.

Introduction: This study aimed to evaluate the prognostic value of the Mayo additive staging system (MASS) and minimal residual disease (MRD) in newly diagnosed multiple myeloma (NDMM) patients., Methods: A total of 238 NDMM patients were enrolled in Beijing Chaoyang Hospital. Fluorescence in-situ hybridization and next-generation flow cytometry were used to examine cytogenetic abnormalities and MRD, respectively. The patients were classified into three groups to compare the effects on progression-free survival (PFS). Univariate and multivariate analyses were applied to identify the survival-related factors., Results: For MASS group, the PFS was significant difference in MASS I, II, and III patients (p = 0.0006); the patients with sustained MRD-negative, non-sustained MRD-negative, sustained MRD-positive, and non-sustained MRD-positive were divided into Groups 1, 2, 3, and 4, respectively. The Group 1 patients had superior PFS than Groups 2 and 3 patients (p < 0.05), but no difference in PFS was observed for Group 2 versus Group 3, Group 2 versus Group 4, and Group 3 versus Group 4 patients. For the MASS and MRD groups, among Groups 2, 3, and 4, MASS I patients had a superior PFS, while III patients showed the opposite result. Strikingly, no difference in PFS for Group 1 patients regardless of the MASS stage was observed. Despite being in MASS II and III, the PFS of Group 1 patients was longer than those with the other three groups. Response to treatment was an independent prognostic factor for MM patients., Conclusion: Patients with an accumulation of high-risk factors and MRD-positive have poor outcomes. Sustained MRD-negative may improve high-risk patients' prognoses., (© 2024 The Author(s). Cancer Medicine published by John Wiley & Sons Ltd.)

The fixation and permeabilization of cells are essential for labeling intracellular biomarkers in flow cytometry. However, these chemical treatments often alter fragile targets, such as cell surface and fluorescent proteins (FPs), and can destroy chemically-sensitive fluorescent labels. This reduces measurement accuracy and introduces compromises into sample workflows, leading to losses in data quality. Here, we demonstrate a novel multi-pass flow cytometry approach to address this long-standing problem. Our technique utilizes individual cell barcoding with laser particles, enabling sequential analysis of the same cells with single-cell resolution maintained. Chemically-fragile protein markers and their fluorochrome conjugates are measured prior to destructive sample processing and adjoined to subsequent measurements of intracellular markers after fixation and permeabilization. We demonstrate the effectiveness of our technique in accurately measuring intracellular FPs and methanol-sensitive antigens and fluorophores, along with various surface and intracellular markers. This approach significantly enhances assay flexibility, enabling accurate and comprehensive cellular analysis without the constraints of conventional one-time measurement flow cytometry. This innovation paves new avenues in flow cytometry for a wide range of applications in immuno-oncology, stem cell research, and cell biology., (© 2024 International Society for Advancement of Cytometry.)

The need for more in-depth exploration of the human immune system has moved the flow cytometry field forward with advances in instrumentation, reagent development and availability, and user-friendly implementation of data analysis methods. We developed a high-quality human 45-color panel, for comprehensive characterization of major cell lineages present in circulation including T cells, γδ T cells, NKT-like cells, B cells, NK cells, monocytes, basophils, dendritic cells, and ILCs. Assay optimization steps are described in detail to ensure that each marker in the panel was optimally resolved. In addition, we highlight the outstanding discernment of cell activation, exhaustion, memory, and differentiation states of CD4+ and CD8+ T cells using this 45-color panel. The panel enabled an in-depth description of very distinct phenotypes associated with the complexity of the T cell memory response. Furthermore, we present how this panel can be effectively used for cell sorting on instruments with a similar optical layout to achieve the same level of resolution. Functional evaluation of sorted specific rare cell subsets demonstrated significantly different patterns of immunological responses to stimulation, supporting functional and phenotypic differences within the T cell memory subsets. In summary, the combination of full spectrum profiling technology and careful assay design and optimization results in a high resolution multiparametric 45-color assay. This panel offers the opportunity to fully characterize immunological profiles present in peripheral blood in the context of infectious diseases, autoimmunity, neurodegeneration, immunotherapy, and biomarker discovery., (© 2024 The Author(s). Cytometry Part A published by Wiley Periodicals LLC on behalf of International Society for Advancement of Cytometry.)

Clinical biomarker strategies increasingly integrate translational research to gain new insights into disease mechanisms or to define better biomarkers in clinical trials. High-dimensional flow cytometry (HDFCM) holds the promise to enhance the exploratory potential beyond traditional, targeted biomarker strategies. However, the increased complexity of HDFCM poses several challenges, which need to be addressed in order to fully leverage its potential and to align with current regulatory requirements in clinical flow cytometry. These challenges include among others extended timelines for assay development and validation, the necessity for extensive knowledge in HDFCM, and sophisticated data analysis strategies. However, no guidelines exist on how to manage such challenges in adopting clinical HDFCM. Our CYTO 2024 workshop "Potential and challenges of clinical high-dimensional flow cytometry" aimed to find consensus across the pharmaceutical industry and broader scientific community on the overall benefits and most urgent challenges of HDFCM in clinical trials. Here, we summarize the insights we gained from our workshop. While this report does not provide a blueprint, it is a first step in defining and summarizing the most pressing challenges in implementing HDFCM in clinical trials. Furthermore, we compile current efforts with the goal to overcome some of these challenges. As such we bring the scientific community and health authorities together to build solutions, which will accelerate and simplify the full adoption of HDFCM in clinical trials., (© 2024 International Society for Advancement of Cytometry.)

Flow cytometry is a powerful analytical technique for measuring the physical and chemical properties of cells or particles as they flow through a beam of light in a fluid stream. It is widely used in several research fields for a wide variety of purposes. This article provides a concise guide to the principles and utilization of flow cytometry. Step-by-step instructions, from instrument setup to data analysis, are intended to help researchers successfully apply flow cytometry in their studies., Competing Interests: Declaration of Competing Interests The authors declare no conflict of interest., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

Since its introduction in animal andrology, flow cytometry (FC) has dramatically evolved. Nowadays, many compartments and functions of the spermatozoa can be analyzed in thousands of spermatozoa, including, but not limited to DNA, acrosome, membrane integrity, membrane symmetry, permeability, and polarity; mitochondrial mass and mitochondrial membrane potential, identification of reactive oxygen species, ion dynamics, and cellular signaling among many others. Improved machines, many more probes, and new software are greatly expanding the amount of information that can be obtained from each flow cytometry analysis. Modern flow cytometers permit the simultaneous investigation of many different sperm compartments and functions and their interactions, allowing the identification of sperm phenotypes, helping to disclose different sperm populations within the ejaculate. Complex flow cytometry panels require a careful design of the experiment, including selecting probes (fully understanding the characteristics and properties of them) and adequate controls (technical and biological). Ideally, compensation and management of data ("cleaning", transformations, the establishment of gates) are better performed post-acquisition using specific software. Data can be expressed as a percentage of positive cells (typically viability assays), intensity of fluorescence (arbitrary fluorescence units, i.e. changes in intracellular Ca 2+ ) or dim and bright populations (typically assays of membrane permeability or antigen expression). Furthermore, artificial intelligence/self-learning algorithms are improving visualization and management of data generated by modern flow cytometers. In this paper, recent developments in flow cytometry for animal andrology will be briefly reviewed; moreover, a small flow cytometry experiment will be used to illustrate how these techniques can improve data analysis., Competing Interests: Declaration of Competing Interest The authors declare that no conflicts of interest could be perceived to prejudice the reported research., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

Rare cells have an important role in development and disease, and methods for isolating and studying cell subsets are therefore an essential part of biology research. Such methods traditionally rely on labeled antibodies targeted to cell surface proteins, but large public databases and sophisticated computational approaches increasingly define cell subsets on the basis of genomic, epigenomic and transcriptomic sequencing data. Methods for isolating cells on the basis of nucleic acid sequences powerfully complement these approaches by providing experimental access to cell subsets discovered in cell atlases, as well as those that cannot be otherwise isolated, including cells infected with pathogens, with specific DNA mutations or with unique transcriptional or splicing signatures. We recently developed a nucleic acid cytometry platform called 'focused interrogation of cells by nucleic acid detection and sequencing' (FIND-seq), capable of isolating rare cells on the basis of RNA or DNA markers, followed by bulk or single-cell transcriptomic analysis. This platform has previously been used to characterize the splicing-dependent activation of the transcription factor XBP1 in astrocytes and HIV persistence in memory CD4 T cells from people on long-term antiretroviral therapy. Here, we outline the molecular and microfluidic steps involved in performing FIND-seq, including protocol updates that allow detection and whole transcriptome sequencing of rare HIV-infected cells that harbor genetically intact virus genomes. FIND-seq requires knowledge of microfluidics, optics and molecular biology. We expect that FIND-seq, and this comprehensive protocol, will enable mechanistic studies of rare HIV + cells, as well as other cell subsets that were previously difficult to recover and sequence., (© 2024. Springer Nature Limited.)

Purpose: Gorham-Stout disease is a very rare disorder characterized by progressive bone erosion and angiomatous proliferation; its etiopathogenesis is still unknown, and diagnosis is still performed by exclusion criteria. The alteration of bone remodeling activity has been reported in patients; in this study, we characterized circulating osteoclast and osteogenic precursors that could be important to better understand the osteolysis observed in patients., Methods: Flow cytometry analysis of PBMC (Peripheral Blood Mononuclear Cells) was performed to characterize circulating osteoclast and osteogenic precursors in GSD patients (n = 9) compared to healthy donors (n = 55). Moreover, ELISA assays were assessed to evaluate serum levels of bone markers including RANK-L (Receptor activator of NF-κB ligand), OPG (Osteoprotegerin), BALP (Bone Alkaline Phosphatase) and OCN (Osteocalcin)., Results: We found an increase of CD16 - /CD14 + CD11b + and CD115 + /CD14 + CD11b + osteoclast precursors in GSD patients, with high levels of serum RANK-L that could reflect the increase of bone resorption activity observed in patients. Moreover, no significant alterations were found regarding osteogenic precursors and serum levels of BALP and OCN., Conclusion: The analysis of circulating bone cell precursors, as well as of RANK-L, could be relevant as an additional diagnostic tool for these patients and could be exploited for therapeutic purposes., (© 2024. The Author(s), under exclusive licence to Italian Society of Endocrinology (SIE).)

Affibody molecules are small (6-kDa) affinity proteins generated by directed evolution for specific binding to various target molecules. The first step in this workflow involves the generation of an affibody library, which can then be used for selection via multiple display methods. This protocol describes selection from affibody libraries by Escherichia coli cell surface display. With this method, high-diversity libraries of 10 11 can be displayed on the cell surface. The method involves two steps for selection of binders from high-diversity libraries: magnetic-activated cell sorting (MACS) and fluorescence-activated cell sorting (FACS). MACS is used first to enrich the library in target-binding clones and to decrease diversity to a size that can be effectively screened and sorted in the flow cytometer in a reasonable time (typically <10 7 cells). The protocol is based on methodology using an AIDA-I autotransporter for display on the outer membrane, but the general procedures can also be adjusted and used for other types of autotransporters or alternative E. coli display methods., (© 2024 Cold Spring Harbor Laboratory Press.)

Natural killer (NK) cells play a crucial role in the immune system's response against cancer. However, the challenge of obtaining the required quantity of NK cells for effective therapeutic response necessitates the development of strategies for their ex vivo expansion. This study aimed to develop a novel feeder cell line, K562.Clone1, capable of promoting the ex vivo expansion of NK cells while preserving their cytotoxic potential. he K562 leukemic cell line was transduced with mbIL-21 and 4-1BBL proteins to generate K562.Clone1 cells. NK cells were then co-cultured with these feeder cells, and their expansion rate was monitored over 14 days. The cytotoxic potential of the expanded NK cells was evaluated against acute myeloid leukemia blasts and tumor cell lines of leukemia and glial origin. Statistical analysis was performed to determine the significance of the results. The K562.Clone1 co-cultured with peripheral NK showed a significant increase in cell count, with an approximate 94-fold expansion over 14 days. Expanded NK cells demonstrated cytotoxicity against the tested tumor cell lines, indicating preservation of their cytotoxic characteristics. Additionally, the CD56, CD16, inhibitory KIRs, and activation receptors were conserved and present in a well-balanced manner. The study successfully developed a feeder cell line, K562.Clone1, that effectively promotes the expansion of NK cells ex vivo while maintaining their cytotoxic potential. This development could significantly contribute to the advancement of NK cell therapy, especially in Brazil., (Copyright © 2024. Published by Elsevier Inc.)

Introduction: The basophil activation test (BAT) has shown evidence of high sensitivity and high specificity to support the diagnosis of IgE-mediated allergy. It is a functional test that uses live cells analyzed by flow cytometry and thus needs to be performed within 24h of blood collection. BAT has shown to be reproducible and reliable when tested in a clinical diagnostic laboratory with standardized protocols and flow cytometry settings., Areas Covered: In this review, we summarize the evidence to support clinical use of BAT and the next steps required for clinical implementation for an improve clinical care for patients with suspected IgE-mediated food allergy., Expert Opinion: BAT has recently been included in Clinical Guidelines of Food Allergy Diagnosis and its implementation in clinical practice depends largely on availability. Proposed clinical applications of the BAT include: distinction between food allergy and asymptomatic IgE sensitization; determination of food allergic status to peanut, tree nuts and seeds in polysensitized children; evaluation of tolerance to baked egg and baked milk in egg and milk allergic children; identification of patients at high-risk of severe allergic reactions; monitoring for spontaneous resolution of food allergy; confirmation of eligibility for specific treatments of food allergy; prediction and monitoring of response to immunomodulatory treatments.

Background: Extramedullary blast proliferations (EBPs) are known to occur in around 15% of chronic myeloid leukemia (CML) patients in the blast phase. Immunophenotypically, the EBPs are commonly myeloid as compared to the lymphoid. Amongst the lymphoid EBPs, T-lymphoblastic type is considerably rare. Furthermore, the occurrence of EBPs at the initial clinical presentation is extremely rare and such presentations almost always portend the occurrence of an imminent hematological blast crisis shortly., Case: A 25-year-old male presented with abdominal fullness for 1 month. There was no history of abdominal pain, vomiting, jaundice, weight loss, or night sweats. On clinical examination, the patient was found to have pallor and was febrile. There was hepatosplenomegaly and a single, firm, mobile, left posterior cervical lymph node measuring 1.5 × 1 cm was palpable. Routine blood counts revealed anemia, leukocytosis, and thrombocytopenia. A fine-needle aspiration (FNA) from the cervical revealed T-lymphoid EBP, confirmed by flow cytometry. Subsequently, his bone marrow examination revealed a diagnosis of CML with BCR::ABL1 fusion. Thus, a final diagnosis of CML with extramedullary T-lymphoid blast crisis localized to the cervical lymph node was rendered., Conclusions: The present report, besides highlighting the utility of FNA cytology in rendering such challenging diagnoses, also reiterates the significance of ancillary techniques, such as flow cytometry, which play a key role in early diagnosis and exact characterization of such rare and aggressive hematolymphoid neoplasms., (© 2024 Wiley Periodicals LLC.)

Affibody molecules are small (6-kDa) affinity proteins generated by directed evolution for specific binding to various target molecules. The first step in this workflow involves the generation of an affibody library, which can then be used for biopanning using multiple display methods. This protocol describes selection from affibody libraries using display on Staphylococcus carnosus Display of affibodies on staphylococci is very efficient and straightforward because of the single cell membrane and the use of a construct with a constitutive promoter. The workflow involves display of affibody libraries on the surface of S. carnosus cells, followed by screening and selection of binders using fluorescence-activated cell sorting (FACS). The transformation of DNA libraries into S. carnosus is less efficient and more complicated than for Escherichia coli. Because of this, staphylococcal display is suitable for affinity maturation or other protein-engineering efforts that are not dependent on very high diversity, and thus magnetic-activated cell sorting (MACS) is often not required before FACS. However, MACS is an option, and MACS procedures used for E. coli can easily be adapted for use in S. carnosus if needed., (© 2024 Cold Spring Harbor Laboratory Press.)

Context.—: Regulatory T-cell (Treg) detection in peripheral blood, based on flow cytometry, is invaluable for diagnosis and treatment of immune-mediated diseases. However, there is a lack of reliable methods to verify the performance, which is pivotal toward standardization of the Tregs assay., Objective.—: To conduct standardization studies and verify the performance of 3 commercially available reagent sets for the Tregs assay based on flow cytometry and agreement analysis for Treg detection across the different reagent sets., Design.—: The analytical performance of Tregs assay using reagent sets supplied by 3 manufacturers was evaluated after establishing the gating strategy and determining the optimal antibody concentration. Postcollection sample stability was evaluated, as well as the repeatability, reproducibility, reportable range, linearity, and assay carryover. Agreement between the different assays was assessed via Bland-Altman plots and linear regression analysis. The relationship between the frequency of CD4+CD25+CD127low/- Tregs and CD4+CD25+Foxp3+ Tregs was evaluated., Results.—: The postcollection sample stability was set at 72 hours after collection at room temperature. The accuracy, repeatability, reproducibility, and accuracy all met the requirements for clinical analysis. Excellent linearity, with R2 ≥0.9 and no assay carryover, was observed. For reportable range, a minimum of 1000 events in the CD3+CD4+ gate was required for Tregs assay. Moreover, the results for Tregs labeled by antibodies from the 3 manufacturers were in good agreement. The percentage of CD4+CD25+CD127low/- Tregs was closely correlated with CD4+CD25+Foxp3+ Tregs., Conclusions.—: This is the first study to evaluate systematically the measurement performance of Tregs in peripheral blood by flow cytometry, which provides a practical solution to verifying the performance of flow cytometry-based immune monitoring projects in clinical practice., Competing Interests: The authors have no relevant financial interest in the products or companies described in this article., (© 2024 College of American Pathologists.)

Introduction: Single-cell RNA sequencing (scRNAseq) and flow cytometry studies in skin are methodologically complex and costly, limiting their accessibility to researchers worldwide. Ideally, RNA and protein-based analyses should be performed on the same lesion to obtain more comprehensive data. However, current protocols generally focus on either scRNAseq or flow cytometry of healthy skin., Methods: We present a novel label-free sample multiplexing strategy, building on the souporcell algorithm, which enables scRNAseq analysis of paired blood and skin samples. Additionally, we provide detailed instructions for simultaneous flow cytometry analysis from the same sample, with necessary adaptations for both healthy and inflamed skin specimens., Results: This tissue multiplexing strategy mitigates technical batch effects and reduces costs by 2-4 times compared to existing protocols. We also demonstrate the effects of varying enzymatic incubation durations (1, 3, and 16 hours, with and without enzyme P) on flow cytometry outcomes. Comprehensive explanations of bioinformatic demultiplexing steps and a detailed step-by-step protocol of the entire experimental procedure are included., Discussion: The protocol outlined in this article will make scRNAseq and flow cytometry analysis of skin samples more accessible to researchers, especially those new to these techniques., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Khoshbakht, Albayrak, Tiryaki, Ağcaoğlu, Öktem, Pınar Sun, Er Gülbezer, Seda Ertekin, Boyvat, Vural and Vural.)

We developed a flow cytometry (FC) assay enabling the rapid and accurate identification of bacterial and viral infections using whole blood samples. The streamlined flow cytometry assay is designed to be user-friendly, making it accessible even for operators with limited experience in FC techniques. The key components of the assay focus on the expression levels of specific surface markers-CD64 on polymorphonuclear neutrophils (PMN) as a marker for bacterial infection, and CD169 on monocytes (MO) for viral infection. The strong performance indicated by an area under the receiver operating characteristic (ROC) curve of 0.94 for both PMN CD64 positive predictive value (PPV) 97.96% and negative predictive value (NPV) 76.67%, and MO CD169 PPV 82.6% and NPV 86.9%, highlight the assay's robustness in differentiating between bacterial and viral infections accurately. The FC assay includes the assessment of immune system status through HLA-DR and IL-1R2 modulation in MO, providing a useful insight into the patients' immune response. The significant increase in the frequency of MO exhibiting reduced HLA-DR expression and elevated IL-1R2 levels in infected patients (compared to healthy controls) underscores the potential of these markers as indicators of infection severity. Although the overall correlation between HLA-DR and IL-1R2 expression levels was not significant across all patients, there was a trend in patients with more severe disease suggesting that these markers may have the potential to assist in stratifying patient risk. The present FC assay has the potential to become routine in the clinical microbiology laboratory community and to be helpful in guiding clinical decision making.

Objective: Flow cytometry (FC) is probably the most important technique for single-cell analysis. It's precisely, rapid, and suitable for multidimensional single-cell analysis. The commonly used side scatter (SSC) intensity determined by FC is often interpreted as a measure of the internal cellular complexity of cells. In simple terms, the more structured a cell is, the higher the SSC intensity quantified by FC. Nevertheless, most of the studies that support this interpretation are based on data derived from animal or human cell lines and while it is assumed that the results can also be transferred to plant or algal cell lines, the details remain unclear. The objective of the recent work is to clarify the interpretation of the SSC signal from algal cells., Results: Algal lipid droplets and their starch play an inherent role to shape the popular SSC signal derived from FC. This was shown by a theoretical approach based on Lorenz-Mie theory. These results were supported by experiments with different model cultures of Chlamydomonas reinhardtii in which a high linear correlation was observed between the SSC signal and the 'physical' starch quantity., (© 2024. The Author(s).)

Platelets play a crucial role in blood transfusions, and understanding the changes that occur during their storage is important for maintaining the quality of preparations. In this study, we examined key alternating factors, with a particular focus on platelet activation and the release of extracellular vesicles. Additionally, we compared two detection methods-imaging flow cytometry (IFC) and nanoparticle tracking analysis (NTA)-for their effectiveness in detecting particles. Platelet concentrates were prepared by pooling buffy coats from five blood group-compatible donors in an additive solution. Samples were analysed after one, three, and seven days of storage for residual white blood cells (WBCs), glucose levels, platelet activation, and extracellular vesicle concentrations. Over the storage period, the total platelet concentration decreased slightly, while the residual WBC count remained stable. Glucose levels declined, whereas platelet activation and extracellular vesicle concentration increased, with a positive correlation between the two. The particle size remained relatively unchanged throughout the storage period. Ultimately, despite controlled processing and storage conditions, platelet activation, and the release of extracellular vesicles still occurred, which may have implications for transfusion recipients. Although an optimised method is still needed, IFC has proved to be specific and potentially appropriate for detecting extracellular vesicles in transfusion preparations.

Current malaria diagnostics are invasive, lack sensitivity, and rapid tests are plagued by deletions in target antigens. Here we introduce the Cytophone, an innovative photoacoustic flow cytometer platform with high-pulse-rate lasers and a focused ultrasound transducer array to noninvasively detect and identify malaria-infected red blood cells (iRBCs) using specific wave shapes, widths, and time delays generated from the absorbance of laser energy by hemozoin, a universal biomarker of malaria infection. In a population of Cameroonian adults with uncomplicated malaria, we assess our device for safety in a cross-sectional cohort (n = 10) and conduct a performance assessment in a longitudinal cohort (n = 20) followed for 30 ± 7 days after clearance of parasitemia. Longitudinal cytophone measurements are compared to point-of-care and molecular assays (n = 94). Cytophone is safe with 90% sensitivity, 69% specificity, and a receiver-operator-curve-area-under-the-curve (ROC-AUC) of 0.84, as compared to microscopy. ROC-AUCs of Cytophone, microscopy, and RDT compared to quantitative PCR are not statistically different from one another. The ability to noninvasively detect iRBCs in the bloodstream is a major advancement which offers the potential to rapidly identify both the large asymptomatic reservoir of infection, as well as diagnose symptomatic cases without the need for a blood sample., (© 2024. The Author(s).)

Both microplastics and phytoplankton are found together in the ocean as suspended microparticles. There is a need for deployable technologies that can identify, size, and count these particles at high throughput to monitor plankton community structure and microplastic pollution levels. In situ analysis is particularly desirable as it avoids the problems associated with sample storage, processing, and degradation. Current technologies for phytoplankton and microplastic analysis are limited in their capability by specificity, throughput, or lack of deployability. Little attention has been paid to the smallest size fraction of microplastics and phytoplankton below 10 μm in diameter, which are in high abundance. Impedance cytometry is a technique that uses microfluidic chips with integrated microelectrodes to measure the electrical impedance of individual particles. Here, we present an impedance cytometer that can discriminate and count microplastics sampled directly from a mixture of phytoplankton in a seawater-like medium in the 1.5-10 μm size range. A simple machine learning algorithm was used to classify microplastic particles based on dual-frequency impedance measurements of particle size (at 1 MHz) and cell internal electrical composition (at 500 MHz). The technique shows promise for marine deployment, as the chip is sensitive, rugged, and mass producible.

Background: Epstein-Barr virus (EBV) specific T-cell response measurement can help adjust immunosuppression in transplant patients with persistent infections. We aim to define T-cell responses against EBV in a cohort of pediatric liver-transplant patients., Methods: Thirty-eight immunosuppressed pediatric liver-transplant patients (IP) and 25 EBV-seropositive healthy-adult controls (HC) were included in our cross-sectional study. Based on their EBV serological (S) and viral load (VL) status, patients were categorized into IP-S NEG , IP-S POS VL NEG and IP-S POS VL POS groups. T-cell response was assessed at two timepoints by stimulating cells with EBV peptides (PepTivator ® ) and performing intracellular-cytokine and activation-induced marker staining. Background subtraction was used to determine EBV-specific T-lymphocyte frequency., Results: Polyfunctional CD8+ T cells indicated previous EBV contact (IP-S NEG 0.00% vs IP-S POS 0.04% and HC 0.02%; p=0.001 and p=0.01, respectively). Polyfunctional CD8+CD107a+IFNɣ+IL2-TNFα- profile was increased in serology-positive (IP-S NEG 0.01% vs IP-S POS 0.13% and HC 0.03%; p=0.01 and p=0.50, respectively) and viral-load positive (IP-S POS VL POS 0.43% vs IP-S POS VL NEG 0.07% and HC 0.03%; p=0.03 and p=0.001, respectively) patients. Central-memory cells were increased among serology-positive adults (IP-S NEG 0.00% vs IP-S POS 0.13% and HC 4.33%; p=0.58 and p=0.002, respectively). At the second timepoint, IP-S NEG patients remained negative (first visit 0.01% vs second visit 0.00%, p=0.44). On the other hand, IP-S POS VL POS patients had cleared viral loads and, subsequently, decreased polyfunctional CD8+CD107a+IFNɣ+IL2-TNFα- cells (first visit 0.43% vs second visit 0.10%, p=0.81)., Conclusion: Polyfunctional CD8+ EBV-specific T-cell response allows detecting EBV previous contact in liver-transplant children. %CD8+CD107a+IFNɣ+IL2-TNFα- is increased in patients with positive viral loads. Central memory CD4+ T-cell population more effectively determines prior EBV-exposure in adults., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2024 Cuesta-Martín de la Cámara, Torices-Pajares, Miguel-Berenguel, Reche-Yebra, Frauca-Remacha, Hierro-Llanillo, Muñoz-Bartolo, Lledín-Barbacho, Gutiérrez-Arroyo, Martínez-Feito, López-Granados and Sánchez-Zapardiel.)

Prostate cancer (PCa) is the second most common cancer among men and the fifth leading cause of cancer death. Circulating tumor cell (CTC) enumeration and characterisation in PCa has been shown to provide valuable information on prognosis of disease, therapy management and detection of resistance. Here, Cellsway's microfluidic platform for high-throughput enrichment of intact CTC populations was used to isolate CTCs from the blood of 20 localised PCa patients and 10 healthy donor samples to evaluate the clinical performance of the technology. To enumerate and characterise CTCs, a multi-parameter flow cytometry analysis was performed on the enriched CTC suspension using CTC-specific biomarkers. CTCs were detected in 17 of 20 patient samples, which corresponds to 85% CTC positivity. The median CTC count per 7.5 ml blood was 2 (1-9). In 80% of patients (n = 16), the number of CTCs ranged from 1 to 5, and in 5% of patients (n = 1) the number of CTCs was above 5. No CTCs were observed in the blood samples of 10 healthy volunteers, demonstrating the high specificity and low risk of false positives of the technology., Competing Interests: The authors have read the journal’s policy and the authors of this manuscript have the following competing interests: EÖ, ŞŞ, NE, EM, BŞD, ÖZ and HK are employees of Mikro Biyosistemler A.S. MKilercik, MKolay and CC are employees of Acibadem Labmed Clinical Laboratories. The authors would like to declare the following patents/patent applications associated with this research: The microfluidic CTC enrichment chip used in this study is related to the patent (US 12,036,553 B2) and is under development as a commercial product by Mikro Biyosistemler A.S. This does not alter our adherence to PLOS ONE policies on sharing data and materials., (Copyright: © 2024 Kilercik et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Most biosensing techniques require complex processing steps that generate prolonged workflows and introduce potential points of error. Here, we report an acoustic pipette to purify and label biomarkers in 70 minutes. A key aspect of this technology is the use of functional negative acoustic contrast particles (fNACPs), which display biorecognition motifs for the specific capture of biomarkers from whole blood. Because of their large size and compressibility, the fNACPs robustly trap along the pressure antinodes of a standing wave and separate from blood components in under 60 seconds with >99% efficiency. fNACPs are subsequently fluorescently labeled in the pipette and are analyzed by both a custom, portable fluorimeter and flow cytometer. We demonstrate the detection of anti-ovalbumin antibodies from blood at picomolar levels (35 to 60 pM) with integrated controls showing minimal nonspecific adsorption. Overall, this system offers a simple and versatile approach for the rapid, sensitive, and specific capture of biomolecules.

Objective: To study the distribution characteristics of natural killer (NK) cells and their subsets in normal peripheral blood in China, and to explore their normal value and significance., Methods: In this study, peripheral blood was collected from 200 healthy adults. Their age range was 18-87 years. All the subjects were divided into 6 age groups: 18-30, 31-40, 41-50, 51-60, 61-70, and 71-87 years. With CD16, CD56, CD4, CD19, as surface markers, fluid cytology detection techniques were used to detect NK cells and the relative and absolute counts. SPSS 27.0 was used for systematic analysis of the data, and the measurement data were expressed as mean±standard deviations. A t test, variance analysis or rank sum test were performed to compare the differences between the age groups and the sex groups. The significance level was set at α=0.05, and P < 0.05 was considered statistically significant., Results: The range of NK B cells in the 200 healthy adult subjects was (0.46±0.24)×10 6 /L, that of CD3 - CD56 + NK cells was (13.14±7.56)×10 6 /L, that of CD56 dim CD16 + NK cells was (5.23±3.12)×10 6 /L, that of CD56 bright NK cells was (85.61±7.40)×10 6 /L, and that of NK T cells was (4.16±3.34)×10 6 /L. There were no statistically significant differences in CD3 - CD56 + NK cells and NK T cells with respect to age ( P = 0.417, P =0.217). However, there was a decreasing trend in the number of NK B cells and CD56 dim CD16 + NK cells with increasing age ( r =0.234, P < 0.001; r =0.099, P < 0.001), particularly after the age of 50. Conversely, CD56 bright NK cells showed an increasing trend with age ( r =0.143, P < 0.001)., Conclusion: The detection of NK cells and their subsets has significant reference value for the diagnosis, treatment, and prognosis of autoimmune diseases, infectious diseases, and tumors. This study provides a preliminary reference range for clinical detection of NK cell subsets, but further research with a larger sample size and multi-center trials are needed to confirm these findings.

Modified vaccinia Ankara (MVA) virus is a widely used vaccine platform, making accurate titration essential for vaccination studies. However, the current plaque forming unit (PFU) assay, the standard for MVA titration, is prone to observer bias and other limitations that affect accuracy and precision. To address these challenges, we developed a new flow cytometry-based quantification method using a highly specific monoclonal antibody (mAb) for the detection of MVA-infected cells, as a more accurate titration assay. Through previous work, we serendipitously identified three MVA-specific hybridoma antibody clones, which we characterized through ELISA, immunoblot, and flow cytometry, confirming their specificity for MVA. Sequencing confirmed that each antibody was monoclonal, and mass spectrometry results revealed that all mAbs target the MVA cell surface binding protein (CSBP, MVA105L). We next optimized the titration protocol using the most effective mAb, 33C7 by refining culture conditions and staining protocols to enhance sensitivity and minimize background. Our optimized method demonstrated superior sensitivity, reliability, and reduced processing time when compared with the traditional PFU assay, establishing it as a more accurate and efficient approach for MVA titration.

In an era when ecological and environmental needs and responsibilities apply pressure on the world's countries and sustainability takes centre stage, ecologic/environmental (E/E) laboratories stand as beacons of scientific inquiry, innovating, optimising, and applying various tests for a better knowledge of our natural resources and the quality status of ecosystems. The purpose of this review is to provide an overview of the use of flow cytometry (FC) as a tool for assessing environmental quality, mainly using living organisms and their biological changes as bioindicators. Cytometric approaches applied to both marine and terrestrial ecosystems ensure the detection of biochemical and functional status of the cells composing either an organ thereof or the organism itself. In addition to cytometric evaluations of the biotic matrix, a brief overview of the techniques for the environmental assessment of biotic and abiotic matrices using mass spectrometry is given. The technique involving the continuous monitoring of the chemical and physical parameters of water, sediment, and soil is basically incapable of detecting any additive and synergetic effects of toxicants on living organisms. Therefore, techniques employing bioindicators provide valuable information for environmental diagnosis, and several studies have demonstrated the strong relationship between specific environmental data and cell/organ behaviour.

In this work, we present experimental results of a high-speed label-free imaging cytometry system that seamlessly merges the high-capturing rate and data sparsity of an event-based CMOS camera with lightweight photonic neuromorphic processing. This combination offers high classification accuracy and a massive reduction in the number of trainable parameters of the digital machine-learning back-end. The event-based camera is capable of capturing 1 Gevents/sec, where events correspond to pixel contrast changes, similar to the retina's ganglion cell function. The photonic neuromorphic accelerator is based on a hardware-friendly passive optical spectrum slicing technique that is able to extract meaningful features from the generated spike-trains using a purely analogue version of the convolutional operation. The experimental scenario comprises the discrimination of artificial polymethyl methacrylate calibrated beads, having different diameters, flowing at a mean speed of 0.1 m/sec. Classification accuracy, using only lightweight digital machine-learning schemes has topped at 98.2%. On the other hand, by experimentally pre-processing the raw spike data through the proposed photonic neuromorphic spectrum slicer at a rate of 3 × 10 6 images per second, we achieved an accuracy of 98.6%. This performance was accompanied by a reduction in the number of trainable parameters at the classification back-end by a factor ranging from 8 to 22, depending on the configuration of the digital neural network. These results confirm that neuromorphic sensing and neuromorphic computing can be efficiently merged to a unified bio-inspired system, offering a holistic enhancement in emerging bio-imaging applications., (© 2024. The Author(s).)

Multiplexed flow cytometry, known for its powerful high-throughput identification capability, is widely applied across various biomedical and clinical fields. However, classical flow cytometry relies on multichannel lasers and detectors, which are significant in cost and size, limiting their application in miniaturized assays. Herein, we developed an acoustic streaming-based flow cytometry technique that focuses on multisized microbeads flowing sheathlessly. This method enables the discrimination of particle types and the quantification of target protein concentrations using only a single detector. Microbeads of different sizes exhibit distinct behaviors in the continuous acoustic streaming tunnel, leading to an increased velocity difference during their transition under the laser spot. Consequently, a size detection method based on "velocity stretching" has been established. A multiplex assay of three proteins: cardiac troponin I, creatine kinase-MB and myoglobin, in acute myocardial infarction is performed to validate the feasibility and evaluate the performance of the system. This new multiplexed flow cytometry strategy is expected to enable low-cost and onsite detection of multiple biomarkers.

Rationale: Chronic inflammation plays an important role in alveolar tissue damage in emphysema, but the underlying immune alterations and cellular interactions are incompletely understood. Objectives: To explore disease-specific pulmonary immune cell alterations and cellular interactions in emphysema. Methods: We used single-cell mass cytometry (CyTOF) to compare the immune compartment in alveolar tissue from 15 patients with severe emphysema and 5 control subjects. Imaging mass cytometry (IMC) was applied to identify altered cell-cell interactions in alveolar tissue from patients with emphysema ( n  = 12) compared with control subjects ( n  = 8). Measurements and Main Results: We observed higher percentages of central memory CD4 T cells in combination with lower proportions of effector memory CD4 T cells in emphysema. In addition, proportions of cytotoxic central memory CD8 T cells and CD127 + CD27 + CD69 - T cells were higher in emphysema, the latter potentially reflecting an influx of circulating lymphocytes into the lungs. Central memory CD8 T cells, isolated from alveolar tissue from patients with emphysema, exhibited an IFN-γ response upon anti-CD3 and anti-CD28 activation. Proportions of CD1c + dendritic cells, expressing migratory and costimulatory markers, were higher in emphysema. Importantly, IMC enabled us to visualize increased spatial colocalization of CD1c + dendritic cells and CD8 T cells in emphysema in situ . Conclusions: Using CyTOF, we characterized the alterations of the immune cell signature in alveolar tissue from patients with chronic obstructive pulmonary disease stage III or IV emphysema versus control lung tissue. These data contribute to a better understanding of the pathogenesis of emphysema and highlight the feasibility of interrogating the immune cell signature using CyTOF and IMC in human lung tissue. Clinical trial registered with www.clinicaltrials.gov (NCT04918706).

This study explores methods to isolate high-pure monocytes and optimize the best growth factor concentration to generate monocytes-derived dendritic cells (mo-DCs), subset DC1, which is crucial in immune responses. Three protocols for monocyte isolation from peripheral blood mononuclear cells (PBMCs) were evaluated: three-hour incubation on FBS-coated flasks; an overnight incubation on FBS-coated flasks; and Magnetic Activated Cell Sorting (MACS). Additionally, five different concentrations of human recombinant granulocyte-macrophage colony-stimulating factor (hrGM-CSF) and human recombinant interleukin-4 (hrIL-4) were compared. We used Flow cytometry to assess the isolation, purification, and generation of pure monocytes characterized as CD14 + , and expression of mo-DC classical markers (HLA-DR, CD80, CD83, and CD86). The obtained results show that monocytes isolated with the second method (overnight incubation) had the highest purity (P < 0.0001) but the lowest yield (P > 0.05), balancing purity and cost-effectiveness. A combination of hrGM-CSF and hrIL-4 at 400 U/mL produced the most favorable outcomes, leading to the highest rate of mo-DC generation (P < 0.05). Notably, this concentration resulted in increasing expression of HLA-DR, CD80, and CD86 surface markers in the generated DCs (P < 0.0001), with no changes in CD83 expression levels. In conclusion, this study offers valuable insights into selecting the optimal approach for monocyte isolation and mo-DC generation in various research contexts, providing a foundation for more effective immunological studies., (© 2024. The Author(s).)

Extracellular vesicles (EVs) released by mesenchymal stromal cells (MSCs) contain a set of microRNAs with regenerative and anti-inflammatory roles. Therefore, purified MSC-EVs are envisioned as a next-generation therapeutic option for a wide array of diseases. In this protocol, we report the strategy for successfully sorting EVs from the supernatant of adipose-derived MSCs (ASCs), often used in orthopedics regenerative medicine applications. First, we described the sample preparation, focusing on EV isolation and labeling steps with carboxyfluorescein succinimidyl ester (CFSE) for fluorescence detection; subsequently, we detailed the sorting process, which constitutes the main part of the protocol. In addition to the rules defined by MISEV 2023 and MIFlowCyt EV guidelines, we applied specific experimental conditions concerning nozzle size, frequency, and sheath pressure. Morphological parameters are established using beads of diameters selected to cover the theoretical range of EV size. After ASC-EVs sorting, we performed a purity check of the sorted fraction by re-analyzing it with the sorter and verifying the EV size distribution with the nanoparticle tracking analysis technique. Due to the increasing importance of EVs, having a pure population to study and characterize is becoming crucial. Here, we demonstrate a winner strategy to set up sorting to achieve this goal.

Flow cytometry facilitates the detection of multiple cell parameters simultaneously with a high level of resolution and throughput, enabling in-depth immunological evaluations. High data resolution in flow cytometry depends on multiple factors, including the concentration of reagents used in the staining protocol, and reagent validation and titration should be the first step in any assay optimization. Titration is the process of finding the concentration of the reagent that best resolves a positive signal from the background, with the saturation of all binding sites, and minimal antibody excess. The titration process involves the evaluation of serial reagent dilutions in cells expressing the antigen target for the tested antibody. The concentration of antibody that provides the highest signal to noise ratio is calculated by plotting the percentage of positive cells and the intensity of the fluorescence of the stained cells with respect to the negative events, in a concentration-response curve. The determination of the optimal antibody concentration is necessary to ensure reliable and reproducible results and is required for each sample type, reagent clone and lot, as well as the methods used for cell collection, staining, and storage conditions. If the antibody dilution is too low, the signal will be too weak to be accurately determined, leading to suboptimal data resolution, high variability across measurements, and the underestimation of the frequency of cells expressing a specific marker. The use of excess antibodies could lead to non-specific binding, reagent misuse, and detector overloading with the signal off scale and higher spillover spreading. In this publication, we summarized the titration fundamentals and best practices, and evaluated the impact of using a different instrument, sample, staining, acquisition, and analysis conditions in the selection of the optimal titer and population resolution.

To be able to resolve multiple organelles at high throughput is an incredible achievement. This will have immediate implications in a range of fields ranging from fundamental cell biology to translational medicine. To realize such a high-throughput multicolor interrogation modality, we have developed a light-sheet based flow imaging system that is capable of visualizing multiple sub-cellular components with organelle-level resolution. This is possible due to the unique optical design that combines an illumination system comprising two collinear light sheets illuminating the flowing cells and a dedicated dual-color 4f-detection, enabling simultaneous recording of multiple organelles. The system PSF sections up to 4 parallel microfluidic channels through which cells are flowing, and multicolor images of cell cross-sections are recorded. The data is then computationally processed (filtered using ML algorithm, shift-corrected, and merged) and combined to reconstruct the 3D multicolor volume. System testing is conducted using multicolor fluorescent nano-beads (size ∼ 175 nm) and flow-based imaging parameters (PSF size, motion-blur, flow rate, frame rate, and number of cell-sections) are determined for quality imaging. Drug treatment studies were carried out for healthy and cancerous HeLa cells to check the performance of the proposed system. The cells were treated with a drug (Vincristine, which is known to promote mitochondrial fission in cells), and the same is compared with untreated control cells. The proposed multicolor iLIFE system could screen ∼ 800 cells/min (at a flow speed of 2490 μ m/s), and the drug treatment studies were carried out up to 24 h. Studies showed the disintegration of mitochondrial network and dysfunctional lysosomes and their accumulation at the cell membrane, which is a clear indication of cell apoptosis. Compared to control cells (untreated), the mortality is highest at a concentration of 500 nM post 12 h of drug treatment. With the capability of multiorganelle interrogation and organelle-level resolution, the multicolor iLIFE cytometry system is suitably placed to assist optical imaging and biomedical research., (© 2024. The Author(s).)

High-dimensional cell phenotyping is a powerful tool to study molecular and cellular changes in health and diseases. CyTOF enables high-dimensional cell phenotyping using tens of surface and intra-cellular markers. To utilize the full potential of CyTOF, we need advanced clustering and machine learning methodologies to enable automated gating of the complex data. Here we show that critical modifications to a machine learning based FlowSOM package and precise parameter optimization can enable us to reliably analyze the complex CyTOF data. We show the impact of key parameters on clustering outcomes while addressing bugs within the publicly available package. We modified the FlowSOM pipeline to fix the bugs, enable scalability to handle large datasets and perform parameter optimization. We further validated this modified pipeline on a substantial external immunological dataset demonstrating the need of data-specific tailored parameter optimization to ensure reliable definition and interrogation of immune cell populations associated with immune disorders., Competing Interests: Authors WT, AS, KR and AP are employees of the company AbbVie. The design, conduct, and financial support for this research were provided by AbbVie. AbbVie actively participated in data interpretation, review, and approval of the publication., (Copyright © 2024 Tao, Sinha, Raddassi and Pandit.)

Flow cytometry is a useful and efficient method for the rapid characterization of a cell population based on the optical and fluorescence properties of individual cells. Ideally, the cell population would consist of only healthy viable cells as dead cells can confound the analysis. Thus, separating out healthy cells from dying and dead cells, and any potential debris, is an important first step in analysis of flow cytometry data. While gating of debris can be conducted using measured optical properties, identifying dead and dying cells often requires utilizing fluorescent stains (e.g. Sytox, a nucleic acid stain that stains cells with compromised cell membranes) to identify cells that should be excluded from downstream analyses. These stains prolong the experimental preparation process and use a flow cytometer's fluorescence channels that could otherwise be used to measure additional fluorescent markers within the cells (e.g. reporter proteins). Here we outline a stain-free method for identifying viable cells for downstream processing by gating cells that are dying or dead. AutoGater is a weakly supervised deep learning model that can separate healthy populations from unhealthy and dead populations using only light-scatter channels. In addition, AutoGater harmonizes different measurements of dead cells such as Sytox and CFUs., (© 2024. The Author(s).)