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Flow Cytometry: Applications and Challenges

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: closed (20 January 2026) | Viewed by 28599

Special Issue Editor


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Guest Editor
Laboratory Medicine Unit, Integrated Diagnostic Services—DIDAS, Padova University Hospital, 35128 Padova, Italy
Interests: flow cytometry; hematology; morphology; molecular tests; laboratory medicine; clinical chemistry; cell biology

Special Issue Information

Dear Colleagues,

Nowadays, despite molecular tests and imaging techniques, flow cytometry continues to capture attention. In particular, non-conventional flow cytometry is becoming increasingly intriguing, like imaging flow cytometry and mass cytometry.

Artificial intelligence and precision medicine are pushing medical knowledge to the extreme. In the context of integration, flow cytometry contributes to understanding processes, including functional ones, in both oncological and non-oncological pathologies. The wealth of information we gain from proteomics, genetic sequencing, and high-sensitivity multiparametric flow cytometry has led to new insights into the immune system and signaling pathways, allowing us to better understand diseases. Furthermore, the evaluation of minimal residual disease is also guaranteed by flow cytometry to personalize treatments. Other challenges involve studying the flow cytometry of less invasive materials (such as saliva or sputum) to obtain early information on various pathologies. In recent years, the study of the intestinal microbiota, microenvironment, and extracellular vesicles, with the use of numerous color panels, allowed us to gain insights into the immune system’s modulations, oncological and infectious diseases, and biological therapies, also helping to understand new therapeutic targets.

We welcome submissions, including original papers, and reviews, to explore how flow cytometry can enhance our understanding of pathologies.

Dr. Alessandra Falda
Guest Editor

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Keywords

  • flow cytometry
  • non-conventional flow cytometry
  • hematology
  • morphology
  • molecular tests
  • cell biology
  • immunology
  • target therapy
  • microbiology
  • antigens
  • functional mechanisms
  • new technologies

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Published Papers (12 papers)

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Research

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18 pages, 3407 KB  
Article
FlowCLOc, a New Tool for Selecting the Most Appropriate Antibodies in Flow Cytometry
by Valentina Serra, Valeria Orrù, Sandra Lai, Mariano Dei, Michele Marongiu, Maria Grazia Piras, Francesca Virdis, Matteo Floris, Giuseppe Delogu, Valeria Lodde, Mauro Pala, Maristella Pitzalis, Edoardo Fiorillo and Francesco Cucca
Int. J. Mol. Sci. 2026, 27(4), 1664; https://doi.org/10.3390/ijms27041664 - 9 Feb 2026
Viewed by 955
Abstract
Circulating immune cells are frequently phenotyped by flow cytometry starting from frozen samples. However, cryopreservation can affect marker expression and cell recovery. To understand which antigens are detectable and reliable after sample cryopreservation, we compared 438 antibodies measured on B, T, and NK-enriched [...] Read more.
Circulating immune cells are frequently phenotyped by flow cytometry starting from frozen samples. However, cryopreservation can affect marker expression and cell recovery. To understand which antigens are detectable and reliable after sample cryopreservation, we compared 438 antibodies measured on B, T, and NK-enriched cells and monocytes in frozen lympho-monocytes and blood with the corresponding fresh blood samples. Cryopreservation affected the expression of 283 markers in lympho-monocytes and 262 in blood, modifying them by more than 20% with respect to fresh blood. Thus, it is essential to carefully evaluate antibody performance when working with frozen samples. To maximize the usability of our results, make them publicly accessible and ready to visualize, we created a catalogue of marker expression variability before and after freezing, namely FlowCLOc. This catalogue simplifies flow cytometry panel design, reducing time-consuming preliminary tests to select the most appropriate and specific markers for staining both frozen and fresh samples. Full article
(This article belongs to the Special Issue Flow Cytometry: Applications and Challenges)
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13 pages, 1793 KB  
Article
Improved Bin-Based Basophil Activation Test Facilitates Comparison of Wheat Allergy and Tolerance in Children and Adults
by Johannes Groffmann, Ines Hoppe, Wail Abbas Ahmed, Dietmar Bast, Sophia Brinster, Seda Altintas, Florian Schusta, Kathleen Weigt, Margitta Worm, Kirsten Beyer and Ria Baumgrass
Int. J. Mol. Sci. 2026, 27(4), 1620; https://doi.org/10.3390/ijms27041620 - 7 Feb 2026
Viewed by 636
Abstract
Diagnosing wheat allergy remains challenging due to the use of oral wheat provocations, which implicate risks to patients and highlights the need for safer, non-invasive diagnostic methods. Here, we present the first direct comparison of a pediatric and adult cohort to study wheat [...] Read more.
Diagnosing wheat allergy remains challenging due to the use of oral wheat provocations, which implicate risks to patients and highlights the need for safer, non-invasive diagnostic methods. Here, we present the first direct comparison of a pediatric and adult cohort to study wheat allergy and wheat tolerance using an improved and validated basophil activation test (BAT). Blood samples from 24 children and 26 adults, clinically classified as facing oral food challenges, were analyzed using our bin-based BAT, enabling standardized data analysis and visualization. In children, the BAT showed significantly higher median basophil activation in wheat-allergic compared to wheat-tolerant individuals. Receiver operating characteristic analysis revealed that BAT responses to wheat, gluten, and gliadin extracts (area under the curve (AUC): 0.71–0.73) had greater diagnostic accuracies than extract-based wheat and gluten-specific immunoglobulin E (sIgE) measurements (AUC: 0.69, 0.70). However, Tri a 19-sIgE, showed the highest diagnostic performance (AUC: 0.97). In adults, BAT responses did not differ significantly between allergic and tolerant individuals. The bin-based BAT is a robust and reproducible diagnostic tool for wheat allergy diagnosis with automated data analysis capabilities. Significant differences were only evident in the pediatric cohort, indicating age-related immunological differences in basophil responsiveness or immune sensitization profiles. These differences could be linked to immune system maturation, variations in immunoglobulin E (IgE) avidity, or differential expression of the high-affinity IgE receptor (FcεRI) on basophils. While Tri a 19 sIgE was the best single predictor in children, its clinical utility remains controversial due to conflicting results in the scientific literature. Full article
(This article belongs to the Special Issue Flow Cytometry: Applications and Challenges)
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15 pages, 3006 KB  
Article
Flow Cytometry-Based Monitoring of Microbial Dynamics During Grape Must Fermentation Under Different Inoculation Strategies
by Federico Sizzano, Valentina Bianconi, Eddy Dorsaz, Antoine Boilley, Hélène Berthoud, Nadine Bridy, Laurent Amiet and Gilles Bourdin
Int. J. Mol. Sci. 2026, 27(3), 1414; https://doi.org/10.3390/ijms27031414 - 30 Jan 2026
Viewed by 541
Abstract
We applied flow cytometry (FCM) to monitor microbial dynamics during grape must fermentation at the winery scale. Experiments were performed on Pinot Noir grapes using three distinct winemaking protocols: inoculation with active dried yeast, Pied-de-Cuve, and spontaneous fermentation. FCM enabled the assessment [...] Read more.
We applied flow cytometry (FCM) to monitor microbial dynamics during grape must fermentation at the winery scale. Experiments were performed on Pinot Noir grapes using three distinct winemaking protocols: inoculation with active dried yeast, Pied-de-Cuve, and spontaneous fermentation. FCM enabled the assessment of yeast viability and metabolic activity, as well as the detection and monitoring of viable bacterial populations during alcoholic fermentation. Amplicon-based DNA sequencing was performed to characterize the associated microbial communities and evaluate protocol-specific effects. Trends identified by amplicon sequencing were partially mirrored by patterns observed in unsupervised FCM analysis. Overall, our results indicate that FCM is a practical tool for monitoring microbial dynamics during fermentation, providing near–real-time information that can support monitoring strategies and risk management in winemaking. Full article
(This article belongs to the Special Issue Flow Cytometry: Applications and Challenges)
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19 pages, 5417 KB  
Article
Flow Cytometric Challenges in Plasmacytoid Dendritic Cell (pDC) Identification: Limitation of BDCA-4 (CD304)-Based Gating
by Sarolta Demeter, Tünde Fekete, Beáta Scholtz, Zoltán Veréb, Lajos Kemény, Attila Bácsi and Kitti Pázmándi
Int. J. Mol. Sci. 2025, 26(22), 10979; https://doi.org/10.3390/ijms262210979 - 13 Nov 2025
Viewed by 1536
Abstract
Plasmacytoid dendritic cells (pDCs) are a unique subset of dendritic cells specialized in rapid and robust type I interferon (IFN) production, playing critical roles in the pathogenesis and pathomechanisms of many human diseases. Accurate identification of pDCs in peripheral blood mononuclear cells (PBMCs) [...] Read more.
Plasmacytoid dendritic cells (pDCs) are a unique subset of dendritic cells specialized in rapid and robust type I interferon (IFN) production, playing critical roles in the pathogenesis and pathomechanisms of many human diseases. Accurate identification of pDCs in peripheral blood mononuclear cells (PBMCs) is challenging due to dynamic and non-exclusive specific expression of surface markers such as blood dendritic cell antigen (BDCA)-2 and BDCA-4. Although BDCA-4 is generally more stably expressed than BDCA-2, prolonged stimulation or inflammatory conditions can induce its expression on multiple non-pDC cell types, reducing the accuracy of pDC identification. Here, we thoroughly investigated BDCA-4 expression dynamics on pDCs and other PBMC subsets following prolonged activation with Toll-like receptor (TLR) 7 and TLR9 agonists. Our flow cytometry analysis revealed a significant increase in BDCA-4-positive non-pDC populations after extended stimulation, primarily corresponding to CD14+ monocytes. To overcome this limitation, we performed a gating strategy combining BDCA-4 positivity with a cocktail of non-pDC markers, enabling the exclusion of non-pDCs and accurate identification of pDCs. This approach enables the reliable identification of pDCs within heterogeneous cell populations using only two fluorescent channels in healthy conditions and even during strong activation or pathological states characterized by chronic inflammation. Full article
(This article belongs to the Special Issue Flow Cytometry: Applications and Challenges)
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16 pages, 2604 KB  
Article
Flow Cytometric Quantification of Mitochondrial Properties: A High-Throughput Approach for Single Organelle Analysis
by Andrew J. Piasecki, Hannah C. Sheehan, Jonathan L. Tilly and Dori C. Woods
Int. J. Mol. Sci. 2025, 26(12), 5481; https://doi.org/10.3390/ijms26125481 - 7 Jun 2025
Viewed by 3656
Abstract
Recent advances in flow cytometry facilitate the detection of subcellular components, such as organelles and vesicles. Fluorescence-activated mitochondria sorting (FAMS) is a flow cytometry-based technique that allows for quantitative analysis and sorting of mitochondria as individual organelles from various tissues and in vitro [...] Read more.
Recent advances in flow cytometry facilitate the detection of subcellular components, such as organelles and vesicles. Fluorescence-activated mitochondria sorting (FAMS) is a flow cytometry-based technique that allows for quantitative analysis and sorting of mitochondria as individual organelles from various tissues and in vitro cell culture. This manuscript details three novel applications of this technique to study mitochondrial function on an organelle-specific level, which is not possible with other approaches. Specifically, we detail the further development and versatility of this nanoscaled flow cytometry approach, including assays to quantitatively assess mitochondrial subpopulations, mitochondrial protein translocation, and both free-floating and EV-encapsulated secreted mitochondria. We demonstrate a multi-parameter quantitative assay for the analysis of mitochondrial autophagy using antibodies targeting the proteins PINK1 and Parkin corresponding to ΔΨM and further show how these can be assessed for mtDNA content on a single organelle level. Further, we establish parameters for the size and surface marker-based analysis of EVs, many of which contain identifiable and respiring mitochondria, as well as free-floating respiratory-competent mitochondria. These results display the versatility of nanoscaled flow cytometry in terms of both sample input and target organelle and provide an important methodological means for the quantitative assessment of mitochondrial features. Full article
(This article belongs to the Special Issue Flow Cytometry: Applications and Challenges)
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19 pages, 3292 KB  
Article
Analysis of Antigen Expression in T-Cell Acute Lymphoblastic Leukemia by Multicolor Flow Cytometry: Implications for the Detection of Measurable Residual Disease
by Alexandra Semchenkova, Ekaterina Mikhailova, Irina Demina, Julia Roumiantseva, Alexander Karachunskiy, Galina Novichkova and Alexander Popov
Int. J. Mol. Sci. 2025, 26(5), 2002; https://doi.org/10.3390/ijms26052002 - 25 Feb 2025
Cited by 4 | Viewed by 2803
Abstract
Multicolor flow cytometry (MFC) is a key method for assessing measurable residual disease (MRD) in acute lymphoblastic leukemia (ALL). However, very few approaches were developed for MRD in T-cell ALL (T-ALL). To identify MRD markers suitable for T-ALL, we analyzed the expression of [...] Read more.
Multicolor flow cytometry (MFC) is a key method for assessing measurable residual disease (MRD) in acute lymphoblastic leukemia (ALL). However, very few approaches were developed for MRD in T-cell ALL (T-ALL). To identify MRD markers suitable for T-ALL, we analyzed the expression of CD2, CD3, CD4, CD5, CD7, CD8, CD10, CD34, CD45, CD48, CD56, CD99, and HLA-DR in T-ALL patients at diagnosis. The median fluorescence intensities (MFIs) of surface CD3, CD4, CD5, CD7, CD8, CD45, CD48, CD99, and CD16+CD56 were also evaluated at Day 15 and the end-of-induction (EOI). The MFC data from 198 pediatric T-ALL patients were analyzed retrospectively. At diagnosis, the most common antigens were identified, and the MFI of T-lineage antigens in blasts was compared to that in T lymphocytes. At follow-up, the MFIs of the proposed MRD markers were compared to those observed at diagnosis. The most common T-ALL antigens were CD7 (100.0%), intracellular CD3 (100.0%), CD45 (98.5%), and CD5 (90.9%). The MFIs of T-lineage antigens in blasts differed significantly from those in T lymphocytes. By the EOI, a substantial modulation of sCD3, CD4, CD5, CD7, CD8, and CD45 was observed. CD48 and CD99 were the most stable markers. The proposed MRD markers (sCD3, CD4, CD5, CD7, CD8, CD45, CD48, CD99, CD16+CD56) enabled MFC-MRD monitoring in virtually all T-ALL patients. Full article
(This article belongs to the Special Issue Flow Cytometry: Applications and Challenges)
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17 pages, 1836 KB  
Article
Clustering Algorithm-Driven Detection of TRBC1-Restricted Clonal T-Cell Populations Produces Better Results than Manual Gating Analysis
by Simon Buček, Andreja Brožič, Simona Miceska, Gorana Gašljević and Veronika Kloboves Prevodnik
Int. J. Mol. Sci. 2025, 26(1), 170; https://doi.org/10.3390/ijms26010170 - 28 Dec 2024
Cited by 4 | Viewed by 2784
Abstract
Flow cytometric (FC) immunophenotyping and T-cell receptor (TCR) gene rearrangement studies are essential ancillary methods for the characterisation of T-cell lymphomas. Traditional manual gating and polymerase chain reaction (PCR)-based analyses can be labour-intensive, operator-dependent, and have limitations in terms of sensitivity and specificity. [...] Read more.
Flow cytometric (FC) immunophenotyping and T-cell receptor (TCR) gene rearrangement studies are essential ancillary methods for the characterisation of T-cell lymphomas. Traditional manual gating and polymerase chain reaction (PCR)-based analyses can be labour-intensive, operator-dependent, and have limitations in terms of sensitivity and specificity. The objective of our study was to investigate the efficacy of the Phenograph and t-SNE algorithms together with an antibody specific for the TCR β-chain constant region 1 (TRBC1) to identify monoclonal T-cell populations. FC- and PCR-based clonality analyses were performed on 275 samples of T-cell lymphomas, B-cell lymphomas, and reactive lymphocytic proliferations. Monotypic T-cell populations were identified in 65.1% of samples by manual gating and 72.4% by algorithm-driven analysis, while PCR-based analysis detected clonal T cells in 68.0%. Of the 262 monotypic populations identified, 46.6% were classified as T-cell lymphomas and 53.4% as T-cell populations of uncertain significance (T-CUS). Algorithm-driven gating identified monotypic populations that were overlooked by manual gating or PCR-based methods. The study highlights the difficulty in distinguishing monotypic populations as T-cell lymphoma or T-CUS. Further research is needed to establish criteria for distinguishing between these populations and to improve FC diagnostic accuracy. Full article
(This article belongs to the Special Issue Flow Cytometry: Applications and Challenges)
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13 pages, 9132 KB  
Article
Fluorescent Aerolysin (FLAER) Binding Is Abnormally Low in the Clonal Precursors of Acute Leukemias, with Binding Particularly Low or Absent in Acute Promyelocytic Leukemia
by María Beatriz Álvarez Flores, María Sopeña Corvinos, Raquel Guillén Santos and Fernando Cava Valenciano
Int. J. Mol. Sci. 2024, 25(22), 11898; https://doi.org/10.3390/ijms252211898 - 5 Nov 2024
Cited by 1 | Viewed by 2808
Abstract
Flow cytometry plays a fundamental role in the diagnosis of leukemias and lymphomas, as well as in the follow-up and evaluation of minimally measurable disease after treatment. In some instances, such as in the case of acute promyelocytic leukemia (APL), rapid diagnosis is [...] Read more.
Flow cytometry plays a fundamental role in the diagnosis of leukemias and lymphomas, as well as in the follow-up and evaluation of minimally measurable disease after treatment. In some instances, such as in the case of acute promyelocytic leukemia (APL), rapid diagnosis is required to avoid death due to serious blood clotting or bleeding complications. Given that promyelocytes do not express the glycophosphatidylinositol (GPI)-anchored protein CD16 and that deficient CD16 expression is a feature of some CD16 polymorphisms and paroxysmal nocturnal hemoglobinuria (PNH), we included the GPI anchor probe FLAER aerolysin in the APL flow cytometry probe panel. Initial tests showed that FLAER binding was absent in pathological promyelocytes from APL patients but was consistently detected with high intensity in healthy promyelocytes from control bone marrow. FLAER binding was studied in 71 hematologic malignancies. Appropriate control cells were obtained from 16 bone marrow samples from patients with idiopathic thrombocytopenic purpura and non-infiltrated non-Hodgkin’s lymphoma. Compared with the positive FLAER signal in promyelocytes from healthy bone marrow, malignant promyelocytes from APL patients showed weak or negative FLAER binding. The FLAER signal in APL promyelocytes was also lower than that in control myeloid progenitors and precursors from patients with other forms of acute myeloid leukemia (AML), B-cell acute lymphoblastic leukemia, or myelodysplastic syndrome. Minimal measurable disease studies performed in APL patients after treatment found normal promyelocyte expression when minimal measurable disease was negative and FLAER-negative promyelocytes when disease relapse was detected. The inclusion of FLAER in the flow cytometry diagnosis and follow-up of APL could be very helpful. Decreased FLAER binding was found in all cases of APL, confirmed by the detection of the PML-RARA fusion transcript and, to a lesser extent, in the other AMLs studied. This study also revealed FLAER differences in other acute leukemias and even between different precursors (myeloid and lymphoid) from healthy controls. However, the reason for FLAER’s non-binding to the malignant precursors of these leukemias remains unknown, and future studies should explore the possible relation with an immune escape phenomenon in these leukemias. Full article
(This article belongs to the Special Issue Flow Cytometry: Applications and Challenges)
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Review

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62 pages, 5991 KB  
Review
Macrophage Plasticity: Phenotypic and Functional Profiles Across Pathological Microenvironments
by Alessandra Falda
Int. J. Mol. Sci. 2026, 27(12), 5333; https://doi.org/10.3390/ijms27125333 (registering DOI) - 12 Jun 2026
Abstract
Macrophages are highly plastic innate immune cells that adopt context-dependent phenotypes along a continuum, integrating developmental origin with local microenvironmental cues rather than conforming to discrete M1/M2 states. This review delineates the molecular circuits shaping macrophage identity—TLR/cytokine signaling, microRNA networks, metabolic rewiring, and [...] Read more.
Macrophages are highly plastic innate immune cells that adopt context-dependent phenotypes along a continuum, integrating developmental origin with local microenvironmental cues rather than conforming to discrete M1/M2 states. This review delineates the molecular circuits shaping macrophage identity—TLR/cytokine signaling, microRNA networks, metabolic rewiring, and epigenetic mechanisms including histone lactylation—and traces how circulating monocyte subsets contribute to tissue macrophage diversity. We examine macrophage plasticity across a broad disease spectrum—oncology, autoimmune and rheumatic diseases, inflammatory bowel disease, infectious diseases, metabolic disorders, and neurological conditions—showing that the pathogenic phenotype is strikingly context-dependent: for instance, M2-like tumor-associated macrophages promote immune evasion in solid tumors, whereas M1-skewed programs drive tissue damage in autoimmunity. Soluble markers (sCD163, sCD14, soluble mannose receptor) are emerging biomarkers of disease activity and prognosis. High-dimensional flow cytometry and mass cytometry (CyTOF) bridge molecular biology and clinical phenotyping, enabling integrated readouts of surface phenotype, intracellular signaling, and metabolic state. Therapeutic strategies discussed include selective tumor-associated macrophage (TAM) reprogramming, chimeric antigen receptor (CAR)-M cell therapies, and biomaterial-based platforms. Future priorities encompass spatially resolved multi-omics, epigenetic and metabolic targeting, and macrophage-centered vaccine approaches. Standardized cytometry panels will be essential for biomarker-guided stratification and context-specific interventions. Full article
(This article belongs to the Special Issue Flow Cytometry: Applications and Challenges)
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17 pages, 1020 KB  
Review
Quantitative Flow Cytometry—Medical Applications with a Focus on Blood Platelets
by Philippe Poncelet, Thomas Lecompte, Anne Bauters and François Mullier
Int. J. Mol. Sci. 2026, 27(4), 1976; https://doi.org/10.3390/ijms27041976 - 19 Feb 2026
Viewed by 907
Abstract
Flow cytometry, measuring light signals, can be used as a quantitative tool to appreciate the numbers of cell-surface molecules targeted with monoclonal antibodies, among other applications. This has been extensively used for blood cells and especially platelets. This review describes how techniques have [...] Read more.
Flow cytometry, measuring light signals, can be used as a quantitative tool to appreciate the numbers of cell-surface molecules targeted with monoclonal antibodies, among other applications. This has been extensively used for blood cells and especially platelets. This review describes how techniques have evolved over time since the first developments of quantitative flow cytometry at the end of the 20th century. Technological issues are first described, applicable to all types of cells/molecules and largely relying on calibration beads with direct or, preferably, indirect immunofluorescence. The platelet field is then addressed with specific tools devoted to surface antigen quantitation. The array of commercially available kits is provided with their specificity. A panorama of platelet antigens quantified that can be used in the diagnosis workout of platelet disorders is then provided, accompanied by a reminder of the impressive stability of marker expression in normal individuals. Variations are then considered in the light of aging or genetic polymorphisms. Finally, the upcoming use of platelet antigen quantification as a monitoring tool for emerging targeted therapies is evoked. All in all, this review provides a comprehensive story of the evolution of the still too marginally used cell antigen quantification. Full article
(This article belongs to the Special Issue Flow Cytometry: Applications and Challenges)
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18 pages, 1331 KB  
Review
Spectral Flow Cytometry: The Current State and Future of the Technology
by E. A. Astakhova, A. S. Gubaeva, D. A. Naumova, A. E. Egorova, A. A. Maznina, I. G. Rybkina, I. M. Osmanov, D. V. Tabakov, O. N. Mityaeva and P. Yu. Volchkov
Int. J. Mol. Sci. 2025, 26(12), 5911; https://doi.org/10.3390/ijms26125911 - 19 Jun 2025
Cited by 7 | Viewed by 6861
Abstract
Flow cytometry is a powerful and widely used tool for the analysis of various cell populations, but its capabilities are severely limited by the need to apply correction of fluorescent signals from near or similar fluorochromes when analyzing multicolor panels. Spectral flow cytometry [...] Read more.
Flow cytometry is a powerful and widely used tool for the analysis of various cell populations, but its capabilities are severely limited by the need to apply correction of fluorescent signals from near or similar fluorochromes when analyzing multicolor panels. Spectral flow cytometry extends the capabilities of classical cytometry by reading the full fluorescence spectrum of fluorophores and their subsequent spectral separation. This significantly increases the number of markers analyzed in a single panel and thus allows for more in-depth studies of cell populations. In the age of big data analysis, this represents a serious advantage of spectral cytometry and can significantly increase its use in scientific and clinical practice. This review describes the principle of spectral cytometry, advantages and limitations of the method, and summarizes the newest deep immunophenotyping panels developed and validated for spectral cytometry. Full article
(This article belongs to the Special Issue Flow Cytometry: Applications and Challenges)
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Other

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18 pages, 2012 KB  
Protocol
FACS-Based Assessment of Human Hematopoietic Stem and Progenitor Cells
by Tessa Schmachtel, Halvard Bonig and Michael A. Rieger
Int. J. Mol. Sci. 2025, 26(17), 8381; https://doi.org/10.3390/ijms26178381 - 28 Aug 2025
Cited by 2 | Viewed by 3236
Abstract
The existing heterogeneity of the human hematopoietic stem cell (HSC) compartment imposes significant challenges in understanding their physiology and molecular constitution. The hematopoietic system is hierarchically organized, with HSCs at the apex, responsible for maintaining homeostasis by ensuring a life-long supply of blood [...] Read more.
The existing heterogeneity of the human hematopoietic stem cell (HSC) compartment imposes significant challenges in understanding their physiology and molecular constitution. The hematopoietic system is hierarchically organized, with HSCs at the apex, responsible for maintaining homeostasis by ensuring a life-long supply of blood cells. HSCs are highly potent but rare, making their pure isolation challenging. To address this, flow-cytometry-based methods are commonly used to isolate HSCs, bridging the gap between surface marker expression and understanding their functional and molecular properties. However, detailed methodology papers providing practical guidance for the prospective isolation of distinct human hematopoietic stem and progenitor cell (HSPC) populations are rare, hindering reproducible applications across different research groups. Here, we present a comprehensive protocol for isolating multipotent long-term repopulating HSCs (LT-HSCs) and define multipotent progenitor populations (MPPs) from human mobilized peripheral blood (mPB) after leukapheresis using fluorescence-activated cell sorting (FACS). By highlighting the workflow, outlining critical considerations and emphasizing recent advancements in the field, we provide an extensive overview of FACS-based human HSC isolation. This facilitates the enrichment of these rare cells for downstream analysis and enables researchers to improve our understanding of the heterogeneity within the HSC compartment. Full article
(This article belongs to the Special Issue Flow Cytometry: Applications and Challenges)
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