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Pham DL, Gillette AA, Riendeau J, Wiech K, Guzman EC, Datta R, Skala MC. Perspectives on label-free microscopy of heterogeneous and dynamic biological systems. J Biomed Opt 2025; 29:S22702. [PMID: 38434231 PMCID: PMC10903072 DOI: 10.1117/1.jbo.29.s2.s22702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/22/2023] [Accepted: 12/14/2023] [Indexed: 03/05/2024]
Abstract
Significance Advancements in label-free microscopy could provide real-time, non-invasive imaging with unique sources of contrast and automated standardized analysis to characterize heterogeneous and dynamic biological processes. These tools would overcome challenges with widely used methods that are destructive (e.g., histology, flow cytometry) or lack cellular resolution (e.g., plate-based assays, whole animal bioluminescence imaging). Aim This perspective aims to (1) justify the need for label-free microscopy to track heterogeneous cellular functions over time and space within unperturbed systems and (2) recommend improvements regarding instrumentation, image analysis, and image interpretation to address these needs. Approach Three key research areas (cancer research, autoimmune disease, and tissue and cell engineering) are considered to support the need for label-free microscopy to characterize heterogeneity and dynamics within biological systems. Based on the strengths (e.g., multiple sources of molecular contrast, non-invasive monitoring) and weaknesses (e.g., imaging depth, image interpretation) of several label-free microscopy modalities, improvements for future imaging systems are recommended. Conclusion Improvements in instrumentation including strategies that increase resolution and imaging speed, standardization and centralization of image analysis tools, and robust data validation and interpretation will expand the applications of label-free microscopy to study heterogeneous and dynamic biological systems.
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Affiliation(s)
- Dan L. Pham
- University of Wisconsin—Madison, Department of Biomedical Engineering, Madison, Wisconsin, United States
| | | | | | - Kasia Wiech
- University of Wisconsin—Madison, Department of Biomedical Engineering, Madison, Wisconsin, United States
| | | | - Rupsa Datta
- Morgridge Institute for Research, Madison, Wisconsin, United States
| | - Melissa C. Skala
- University of Wisconsin—Madison, Department of Biomedical Engineering, Madison, Wisconsin, United States
- Morgridge Institute for Research, Madison, Wisconsin, United States
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2
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Jin J, Mao X, Zhang D. A differential diagnosis method for systemic CAEBV and the prospect of EBV-related immune cell markers via flow cytometry. Ann Med 2024; 56:2329136. [PMID: 38502913 PMCID: PMC10953786 DOI: 10.1080/07853890.2024.2329136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 02/23/2024] [Indexed: 03/21/2024] Open
Abstract
Chronic active Epstein-Barr virus (CAEBV) infection of the T-cell or Natural killer (NK)-cell type, systemic form (systemic CAEBV or sCAEBV) was defined by the WHO in 2017 as an EBV-related lymphoproliferative disorder and is listed as an EBV-positive T-cell and NK-cell proliferation. The clinical manifestations and prognoses are heterogeneous. This makes systemic CAEBV indistinguishable from other EBV-positive T-cell and NK-cell proliferations. Early diagnosis of systemic CAEBV and early hematopoietic stem cell transplantation can improve patient prognosis. At present, the diagnosis of systemic CAEBV relies mainly on age, clinical manifestations, and cell lineage, incurring missed diagnosis, misdiagnosis, long diagnosis time, and inability to identify high-risk systemic CAEBV early. The diagnostic methods for systemic CAEBV are complicated and lack systematic description. The recent development of diagnostic procedures, including molecular biological and immunological techniques such as flow cytometry, has provided us with the ability to better understand the proliferation of other EBV-positive T cells and NK cells, but there is no definitive review of their value in diagnosing systemic CAEBV. This article summarizes the recent progress in systemic CAEBV differential diagnosis and the prospects of flow cytometry.
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Affiliation(s)
- Jie Jin
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xia Mao
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Donghua Zhang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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Brett VE, Dignat George F, James C. Circulating endothelial cells in pathophysiology. Curr Opin Hematol 2024; 31:148-154. [PMID: 38362895 DOI: 10.1097/moh.0000000000000814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
PURPOSE OF REVIEW The purpose of this review is to synthesize recent insights into the roles and importance of circulating endothelial cells (CECs) as indicators of the severity, progression, and prognosis of vascular-related diseases. RECENT FINDINGS Recent studies have identified elevated counts of CECs in pathological conditions, notably inflammatory or cardiovascular diseases such as acute myocardial infarction and heart failure, underscoring their potential as sensitive indicators of disease. Furthermore, the rise in CEC levels in cancer patients, particularly with disease advancement, points to their role in cancer-associated angiogenesis and response to treatment. SUMMARY This review underscores the evolving significance of CECs as markers for evaluating the gravity and advancement of diseases with vascular injury, including cardiovascular diseases, cancer, inflammatory conditions, and thromboembolic events. These last years, efforts made to standardize flow cytometry detection of CEC and the development of highly sensitive techniques to isolate, quantify or phenotype rare cells open promising avenues for clinical application. This may yield extensive knowledge regarding the mechanisms by which endothelial cells contribute to a variety of vascular-related disorders and their clinical value as emerging biomarkers.
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Affiliation(s)
- Victor Emmanuel Brett
- University of Bordeaux, Institut national de la santé et de la recherche médicale, Biologie des maladies cardio-vasculaires, U1034
- Laboratory of Hematology, Bordeaux University Hospital, Pessac
| | - Francoise Dignat George
- Aix Marseille Univ, INSERM, INRAE, C2VN, UFR de Pharmacie
- Hematology and Vascular Biology Department, CHU La Conception, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Chloe James
- University of Bordeaux, Institut national de la santé et de la recherche médicale, Biologie des maladies cardio-vasculaires, U1034
- Laboratory of Hematology, Bordeaux University Hospital, Pessac
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4
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Chen K, Zhang Y, Li C, Liu Y, Cao Q, Zhang X. Clinical value of molecular subtypes identification based on anoikis-related lncRNAs in castration-resistant prostate cancer. Cell Signal 2024; 117:111104. [PMID: 38373667 DOI: 10.1016/j.cellsig.2024.111104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 12/07/2023] [Accepted: 02/15/2024] [Indexed: 02/21/2024]
Abstract
BACKGROUND Anoikis is a distinctive type of apoptosis. It is involved in tumor progression and metastasis. But its function in castration-resistant prostate cancer (CRPC) remains veiled. We aimed to develop a prognostic indicator based on anoikis-related long non-coding RNAs (arlncRNAs) and to investigate their biological function in CRPC. MATERIAL AND METHOD Differentially expressed anoikis-related genes were extracted from two CRPC datasets, GSE51873, and GSE78201. Four lncRNAs associated with the anoikis-related genes were selected. A risk model based on these lncRNAs was developed and validated in The Cancer Genome Atlas (TCGA) and the Memorial Sloan-Kettering Cancer Center (MSKCC) prostate cancer cohorts. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, immune infiltration, immune checkpoints expression, and drug susceptibility were performed based on the model. To identify the biofunction of anoikis-related lncRNA, CCK-8 assays, colony formation assays, and flow cytometry were used. RESULT Twenty-nine anoikis-related genes were differentially expressed in the CRPC datasets. And 36 prognostic arlncRNAs were selected for the LASSO Cox analysis. Patients were subsequently classified into two subtypes by constructing an anoikis-related lncRNA based prognostic index (ARPI). The accuracy of this index was validated. KEGG enrichment analysis revealed that the high-ARPI group was enriched in cancer-related and immune-related pathways. Immune infiltration analysis has indicated a positive association between high-ARPI groups and increased immune infiltration. Fulvestrant, OSI-027, Lapatinib, Dabrafenib, and Palbociclib were identified as potential sensitive drugs for high-ARPI patients. In vitro experiments exhibited that silencing LINC01138 dampened the proliferation, migration and enzalutamide resistance in CRPC. Furthermore, it stimulated apoptosis and inhibited the eithelial-mesenchymal transition process. CONCLUSION Four arlncRNAs were identified and a risk model was established to predict the prognosis of patients with prostate cancer. Immune infiltration and drug susceptibility analysis revealed a potential therapeutic strategy for patients with castration-resistant prostate cancer.
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Affiliation(s)
- Kailei Chen
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Institute of Urology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Yunxuan Zhang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Institute of Urology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Chengyong Li
- Department of Urology, the Second Hospital of Shanxi Medical University, Taiyuan 030000, China
| | - Yuenan Liu
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Institute of Urology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Qi Cao
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Institute of Urology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
| | - Xiaoping Zhang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Institute of Urology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen 518000, China..
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Kim SY, Huh HJ. Toward Standardization of Flow-Cytometric Immunophenotyping for the Diagnosis and Monitoring of Hematologic Malignancies. Ann Lab Med 2024; 44:193-194. [PMID: 38145894 PMCID: PMC10813827 DOI: 10.3343/alm.2023.0467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023] Open
Affiliation(s)
- Seon Young Kim
- Department of Laboratory Medicine, Chungnam National University College of Medicine, Daejeon, Korea
| | - Hee Jin Huh
- Department of Laboratory Medicine, Dongguk University Ilsan Hospital, Goyang, Korea
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6
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Solomonova E, Shoman N, Akimov A, Rylkova O, Meger Y. Application of confocal microscopy and flow cytometry to identify physiological responses of Prorocentrum micans to the herbicide glyphosate. Mar Environ Res 2024; 196:106417. [PMID: 38394976 DOI: 10.1016/j.marenvres.2024.106417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/25/2024] [Accepted: 02/19/2024] [Indexed: 02/25/2024]
Abstract
The physiological response of the dinoflagellate P. micans to the effect of the herbicide glyphosate at a concentration of 25-200 μg L-1 was evaluated. It has been shown that P. micans is able to grow due to the consumption of dissolved organic phosphorus formed as a result of the mineralization of glyphosate by bacteria. The addition of glyphosate to the medium inhibits the photosynthetic activity of cells; there is a pronounced inhibition of the relative electron transfer rate along the electron transport chain and the maximum quantum efficiency of the use of light energy. Morphological and ultrastructural changes in P. micans cells were evaluated at sublethal (150 μg L-1) and lethal (200 μg L-1) glyphosate concentrations. It has been shown that at a herbicide concentration of 150 μg L-1, the first signs of apoptosis appear in most P. micans cells: a decrease in lateral light scattering, cytoplasmic retraction, partial destruction of cytoplasmic organelles, a change in the morphology of nuclei, mitochondria, a change in the potential of mitochondrial membranes, and a decrease in the autofluorescence of chlorophyll in cells. At a glyphosate concentration of 200 μg L-1, P. micans showed signs of a late stage of apoptosis: violation of the integrity of intracellular organelles and chromatin organization, fragmentation of nuclei, condensation of cytoplasm, disorganization of chloroplasts in the cells, and the release of cell contents beyond the cell membrane. The effectiveness of using flow cytometry and laser scanning confocal microscopy methods for identifying signs and stages of cell apoptosis when exposed to glyphosate is discussed.
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Affiliation(s)
- Ekaterina Solomonova
- A.O. Kovalevsky Institute of Biology of the Southern Seas of the Russian Academy of Sciences, 2, Nahimov Avе., Sevastopol, Russian Federation.
| | - Natalia Shoman
- A.O. Kovalevsky Institute of Biology of the Southern Seas of the Russian Academy of Sciences, 2, Nahimov Avе., Sevastopol, Russian Federation
| | - Arkady Akimov
- A.O. Kovalevsky Institute of Biology of the Southern Seas of the Russian Academy of Sciences, 2, Nahimov Avе., Sevastopol, Russian Federation
| | - Olga Rylkova
- A.O. Kovalevsky Institute of Biology of the Southern Seas of the Russian Academy of Sciences, 2, Nahimov Avе., Sevastopol, Russian Federation
| | - Yakov Meger
- Sevastopol State University, 299053, Universitetskaya Street, 33, Sevastopol, Russian Federation
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7
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Derman BA, Fonseca R. Measurable Residual Disease and Decision-Making in Multiple Myeloma. Hematol Oncol Clin North Am 2024; 38:477-495. [PMID: 38184470 DOI: 10.1016/j.hoc.2023.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2024]
Abstract
Measurable (minimal) residual disease (MRD) has already proven to be one of the most important prognostic factors in multiple myeloma (MM). Each improvement in the depth of MRD testing has led to superior discrimination of outcomes, and sustained MRD negativity seems to be paramount to durable responses. Peripheral blood assays to assess for MRD are still under investigation but hold promise as complementary tools to bone marrow MRD assays such as next-generation sequencing and flow cytometry. Herein, the authors explore the evidence and potential benefits and drawbacks of MRD-adapted clinical decision-making in MM.
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Affiliation(s)
- Benjamin A Derman
- Section of Hematology/Oncology, University of Chicago, 5841 South Maryland Avenue, Chicago, IL 60637, USA.
| | - Rafael Fonseca
- Division of Hematology and Medical Oncology, Mayo Clinic in Arizona, 13400 East Shea Boulevard, MCCRB 3-001, Phoenix, AZ 85259, USA
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8
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Lucero J, Alhumaid M, Novitzky-Basso I, Capo-Chichi JM, Stockley T, Gupta V, Bankar A, Chan S, Schuh AC, Minden M, Mattsson J, Kumar R, Sibai H, Tierens A, Kim DDH. Flow cytometry-based measurable residual disease (MRD) analysis identifies AML patients who may benefit from allogeneic hematopoietic stem cell transplantation. Ann Hematol 2024; 103:1187-1196. [PMID: 38291275 DOI: 10.1007/s00277-024-05639-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/21/2024] [Indexed: 02/01/2024]
Abstract
Measurable residual disease (MRD) monitoring independently predicts long-term outcomes in patients with acute myeloid leukemia (AML). Of the various modalities available, multiparameter flow cytometry-based MRD analysis is widely used and relevant for patients without molecular targets. In the transplant (HCT) setting, the presence of MRD pre-HCT is associated with adverse outcomes. MRD-negative remission status pre-HCT was also associated with longer overall (OS) and progression-free survival and a lower risk of relapse. We hypothesize that the combination of disease risk and MRD at the time of first complete remission (CR1) could identify patients according to the benefit gained from HCT, especially for intermediate-risk patients. We performed a retrospective analysis comparing the outcomes of HCT versus non-HCT therapies based on MRD status in AML patients who achieved CR1. Time-dependent analysis was applied considering time-to-HCT as a time-dependent covariate and compared HCT versus non-HCT outcomes according to MRD status at CR1. Among 336 patients assessed at CR1, 35.1% were MRD positive (MRDpos) post-induction. MRDpos patients benefitted from HCT with improved OS and relapse-free survival (RFS), while no benefit was observed in MRDneg patients. In adverse-risk patients, HCT improved OS (HR for OS 0.55; p = 0.05). In intermediate-risk patients, HCT benefit was not significant for OS and RFS. Intermediate-risk MRDpos patients were found to have benefit from HCT with improved OS (HR 0.45, p = 0.04), RFS (HR 0.46, p = 0.02), and CIR (HR 0.41, p = 0.02). Our data underscore the benefit of HCT in adverse risk and MRDpos intermediate-risk AML patients.
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Affiliation(s)
- Josephine Lucero
- Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada.
| | | | - Igor Novitzky-Basso
- Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Jose-Mario Capo-Chichi
- Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Tracy Stockley
- Division of Clinical Laboratory Genetics, Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
| | - Vikas Gupta
- Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Aniket Bankar
- Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Steven Chan
- Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Andre C Schuh
- Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Mark Minden
- Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Jonas Mattsson
- Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Rajat Kumar
- Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Hassan Sibai
- Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Anne Tierens
- Division of Hematology and Transfusion Medicine, Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
| | - Dennis D H Kim
- Division of Medical Oncology & Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada.
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9
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Schildknecht K, Samans B, Gussmann J, Baron U, Raschke E, Babel N, Oppatt J, Gellhaus K, Rossello A, Janack I, Olek S. Specifications of qPCR based epigenetic immune cell quantification. Clin Chem Lab Med 2024; 62:615-626. [PMID: 37982750 DOI: 10.1515/cclm-2023-1056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 10/25/2023] [Indexed: 11/21/2023]
Abstract
OBJECTIVES Immune monitoring is an important aspect in diagnostics and clinical trials for patients with compromised immune systems. Flow cytometry is the standard method for immune cell counting but faces limitations. Best practice guidelines are available, but lack of standardization complicates compliance with e.g., in vitro diagnostic regulations. Limited sample availability forces immune monitoring to predominantly use population-based reference intervals. Epigenetic qPCR has evolved as alternative with broad applicability and low logistical demands. Analytical performance specifications (APS) have been defined for qPCR in several regulated fields including testing of genetically modified organisms or vector-shedding. METHODS APS were characterized using five epigenetic qPCR-based assays quantifying CD3+, CD4+, CD8+ T, B and NK cells in light of regulatory requirements. RESULTS Epigenetic qPCR meets all specifications including bias, variability, linearity, ruggedness and sample stability as suggested by pertinent guidelines and regulations. The assays were subsequently applied to capillary blood from 25 normal donors over a 28-day period. Index of individuality (IoI) and reference change values were determined to evaluate potential diagnostic gains of individual reference intervals. Analysis of the IoI suggests benefits for individual over population-based references. Reference change values (RCVs) show that changes of approx. Fifty percent from prior measurement are suggestive for clinically relevant changes in any of the 5 cell types. CONCLUSIONS The demonstrated precision, long-term stability and obtained RCVs render epigenetic cell counting a promising tool for immune monitoring in clinical trials and diagnosis.
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Affiliation(s)
- Konstantin Schildknecht
- Ivana Türbachova Laboratory for Epigenetics, Epiontis, Precision for Medicine GmbH, Berlin, Germany
| | - Björn Samans
- Ivana Türbachova Laboratory for Epigenetics, Epiontis, Precision for Medicine GmbH, Berlin, Germany
| | - Jasmin Gussmann
- Ivana Türbachova Laboratory for Epigenetics, Epiontis, Precision for Medicine GmbH, Berlin, Germany
| | - Udo Baron
- Ivana Türbachova Laboratory for Epigenetics, Epiontis, Precision for Medicine GmbH, Berlin, Germany
| | - Eva Raschke
- Ivana Türbachova Laboratory for Epigenetics, Epiontis, Precision for Medicine GmbH, Berlin, Germany
| | - Nina Babel
- Marienhospital Herne, Klinik I für Innere Medizin, Centrum für Translationale Medizin, Herne, Germany
| | - Julia Oppatt
- Ivana Türbachova Laboratory for Epigenetics, Epiontis, Precision for Medicine GmbH, Berlin, Germany
| | | | - Araceli Rossello
- Ivana Türbachova Laboratory for Epigenetics, Epiontis, Precision for Medicine GmbH, Berlin, Germany
| | - Isabell Janack
- Ivana Türbachova Laboratory for Epigenetics, Epiontis, Precision for Medicine GmbH, Berlin, Germany
| | - Sven Olek
- Ivana Türbachova Laboratory for Epigenetics, Epiontis, Precision for Medicine GmbH, Berlin, Germany
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10
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Rea DJ, Miller RS, Crucian BE, Valentine RW, Cristoforetti S, Bearg SB, Sipic Z, Cheng J, Yu R, Calaway KM, Eames D, Nelson ES, Lewandowski BE, Perusek GP, Chan EY. Single drop cytometry onboard the International Space Station. Nat Commun 2024; 15:2634. [PMID: 38528030 DOI: 10.1038/s41467-024-46483-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 02/29/2024] [Indexed: 03/27/2024] Open
Abstract
Real-time lab analysis is needed to support clinical decision making and research on human missions to the Moon and Mars. Powerful laboratory instruments, such as flow cytometers, are generally too cumbersome for spaceflight. Here, we show that scant test samples can be measured in microgravity, by a trained astronaut, using a miniature cytometry-based analyzer, the rHEALTH ONE, modified specifically for spaceflight. The base device addresses critical spaceflight requirements including minimal resource utilization and alignment-free optics for surviving rocket launch. To fully enable reduced gravity operation onboard the space station, we incorporated bubble-free fluidics, electromagnetic shielding, and gravity-independent sample introduction. We show microvolume flow cytometry from 10 μL sample drops, with data from five simultaneous channels using 10 μs bin intervals during each sample run, yielding an average of 72 million raw data points in approximately 2 min. We demonstrate the device measures each test sample repeatably, including correct identification of a sample that degraded in transit to the International Space Station. This approach can be utilized to further our understanding of spaceflight biology and provide immediate, actionable diagnostic information for management of astronaut health without the need for Earth-dependent analysis.
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Affiliation(s)
- Daniel J Rea
- DNA Medicine Institute (DMI), Bedford, MA, USA
- rHEALTH, Bedford, MA, USA
| | | | - Brian E Crucian
- Human Health and Performance Directorate, NASA Johnson Space Center, Houston, TX, USA
| | | | | | - Samuel B Bearg
- DNA Medicine Institute (DMI), Bedford, MA, USA
- rHEALTH, Bedford, MA, USA
| | - Zlatko Sipic
- DNA Medicine Institute (DMI), Bedford, MA, USA
- rHEALTH, Bedford, MA, USA
| | - Jamie Cheng
- DNA Medicine Institute (DMI), Bedford, MA, USA
- rHEALTH, Bedford, MA, USA
| | - Rebecca Yu
- DNA Medicine Institute (DMI), Bedford, MA, USA
- rHEALTH, Bedford, MA, USA
| | | | | | | | | | | | - Eugene Y Chan
- DNA Medicine Institute (DMI), Bedford, MA, USA.
- rHEALTH, Bedford, MA, USA.
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11
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Tang X, Mai H, Wang L, Chen S, Chen F, Li T, Liu Y, Zhou G, Liu S, Wang Y, Liu S, Fu X, Wen F. Diagnostic significance of cerebrospinal fluid flow cytometry in Chinese children with B lineage acute lymphoblastic leukemia. BMC Pediatr 2024; 24:204. [PMID: 38519960 PMCID: PMC10958868 DOI: 10.1186/s12887-024-04684-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 03/01/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND Central nervous system leukemia (CNSL) is one of the major causes of the poor prognosis of childhood leukemia. We aimed to compare the sensitivity of cytomorphology (CM) and flow cytometry (FCM) in diagnosing CNSL, emphasizing the importance of FCM in the diagnosis process. METHODS One-hundred-sixty-five children with newly diagnosed B-cell Acute Lymphoblastic Leukemia (B-cell ALL) were included in this study. Cerebrospinal fluid (CSF) samples were taken for routine CSF analysis, CM analysis, and FCM examination. Computed tomography scans and/or magnetic resonance imaging were performed at diagnosis. Patients with CNS2, CNS3, and traumatic lumbar puncture (TLP) at diagnosis received two additional courses of triple intrathecal injections during induction treatment. We compared the sensitivity of FCM and CM in the diagnosis of children with CNSL. RESULTS One hundred and twenty-eight (77.58%) CSF samples were negative by either CM or FCM (CM-/FCM-), four (2.42%) were positive by both CM and FCM (CM+/FCM+), and thirty-three (20%) displayed a single positive finding by FCM (CM-/FCM+) (p = 0.044). By adding two intrathecal injections in the induction treatment, ten children with TLP+ had no CNS relapse, like those with TLP-. However, compared to CNS1 and TLP, the event-free survival (EFS) did not significantly improve in patients with CNS2 and CNS3. Moreover, CNSL status was associated with worse 3-year EFS (p < 0.05). CONCLUSIONS We have validated that FCM is more accurate in stratifying the status of the CNS compared to CM analysis. However, to improve the EFS rate of childhood leukemia, it is necessary to combine CM examination, FCM, and cranial imaging for the early diagnosis of CNSL.
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Affiliation(s)
- Xue Tang
- Department of Hematology and Oncology, Shenzhen Children's Hospital, No.7019 Yitian Road, Futian District, Shenzhen, China
- Department of Hematology and Oncology, Shenzhen Children's Hospital of China Medical University, Shenzhen, China
| | - Huirong Mai
- Department of Hematology and Oncology, Shenzhen Children's Hospital, No.7019 Yitian Road, Futian District, Shenzhen, China
| | - Lulu Wang
- Department of Hematology and Oncology, Shenzhen Children's Hospital, No.7019 Yitian Road, Futian District, Shenzhen, China
| | - Shiyang Chen
- Department of Laboratory Medicine, Shenzhen Children's Hospital, Shenzhen, China
| | - Fen Chen
- Department of Hematology and Oncology, Shenzhen Children's Hospital, No.7019 Yitian Road, Futian District, Shenzhen, China
| | - Tonghui Li
- Department of Hematology and Oncology, Shenzhen Children's Hospital, No.7019 Yitian Road, Futian District, Shenzhen, China
| | - Yi Liu
- Department of Hematology and Oncology, Shenzhen Children's Hospital, No.7019 Yitian Road, Futian District, Shenzhen, China
| | - Guichi Zhou
- Department of Hematology and Oncology, Shenzhen Children's Hospital, No.7019 Yitian Road, Futian District, Shenzhen, China
| | - Shilin Liu
- Department of Hematology and Oncology, Shenzhen Children's Hospital, No.7019 Yitian Road, Futian District, Shenzhen, China
| | - Ying Wang
- Department of Hematology and Oncology, Shenzhen Children's Hospital, No.7019 Yitian Road, Futian District, Shenzhen, China
| | - Sixi Liu
- Department of Hematology and Oncology, Shenzhen Children's Hospital, No.7019 Yitian Road, Futian District, Shenzhen, China
| | - Xiaoying Fu
- Department of Laboratory Medicine, Shenzhen Children's Hospital, Shenzhen, China.
| | - Feiqiu Wen
- Department of Hematology and Oncology, Shenzhen Children's Hospital, No.7019 Yitian Road, Futian District, Shenzhen, China.
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12
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Seedhom MO, Dersh D, Holly J, Pavon-Eternod M, Wei J, Angel M, Shores L, David A, Santos J, Hickman H, Yewdell JW. Paradoxical imbalance between activated lymphocyte protein synthesis capacity and rapid division rate. eLife 2024; 12:RP89015. [PMID: 38512721 PMCID: PMC10957176 DOI: 10.7554/elife.89015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024] Open
Abstract
Rapid lymphocyte cell division places enormous demands on the protein synthesis machinery. Flow cytometric measurement of puromycylated ribosome-associated nascent chains after treating cells or mice with translation initiation inhibitors reveals that ribosomes in resting lymphocytes in vitro and in vivo elongate at typical rates for mammalian cells. Intriguingly, elongation rates can be increased up to 30% by activation in vivo or fever temperature in vitro. Resting and activated lymphocytes possess abundant monosome populations, most of which actively translate in vivo, while in vitro, nearly all can be stalled prior to activation. Quantitating lymphocyte protein mass and ribosome count reveals a paradoxically high ratio of cellular protein to ribosomes insufficient to support their rapid in vivo division, suggesting that the activated lymphocyte proteome in vivo may be generated in an unusual manner. Our findings demonstrate the importance of a global understanding of protein synthesis in lymphocytes and other rapidly dividing immune cells.
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Affiliation(s)
- Mina O Seedhom
- National Institute of Allergy and Infectious DiseasesBethesdaUnited States
| | - Devin Dersh
- National Institute of Allergy and Infectious DiseasesBethesdaUnited States
| | - Jaroslav Holly
- National Institute of Allergy and Infectious DiseasesBethesdaUnited States
| | | | - Jiajie Wei
- National Institute of Allergy and Infectious DiseasesBethesdaUnited States
| | - Matthew Angel
- National Institute of Allergy and Infectious DiseasesBethesdaUnited States
| | - Lucas Shores
- National Institute of Allergy and Infectious DiseasesBethesdaUnited States
| | - Alexandre David
- CNRS UMR-5203; INSERM U661; UM1; UM2, Institut de Génomique FonctionnelleMontpellierFrance
| | - Jefferson Santos
- National Institute of Allergy and Infectious DiseasesBethesdaUnited States
| | - Heather Hickman
- National Institute of Allergy and Infectious DiseasesBethesdaUnited States
| | - Jonathan W Yewdell
- National Institute of Allergy and Infectious DiseasesBethesdaUnited States
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13
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Zhang S, Han Z, Qi H, Liu S, Liu B, Sun C, Feng Z, Sun M, Duan X. Convolutional Neural Network-Driven Impedance Flow Cytometry for Accurate Bacterial Differentiation. Anal Chem 2024; 96:4419-4429. [PMID: 38448396 DOI: 10.1021/acs.analchem.3c04421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Impedance flow cytometry (IFC) has been demonstrated to be an efficient tool for label-free bacterial investigation to obtain the electrical properties in real time. However, the accurate differentiation of different species of bacteria by IFC technology remains a challenge owing to the insignificant differences in data. Here, we developed a convolutional neural networks (ConvNet) deep learning approach to enhance the accuracy and efficiency of the IFC toward distinguishing various species of bacteria. First, more than 1 million sets of impedance data (comprising 42 characteristic features for each set) of various groups of bacteria were trained by the ConvNet model. To improve the efficiency for data analysis, the Spearman correlation coefficient and the mean decrease accuracy of the random forest algorithm were introduced to eliminate feature interaction and extract the opacity of impedance related to the bacterial wall and membrane structure as the predominant features in bacterial differentiation. Moreover, the 25 optimized features were selected with differentiation accuracies of >96% for three groups of bacteria (bacilli, cocci, and vibrio) and >95% for two species of bacilli (Escherichia coli and Salmonella enteritidis), compared to machine learning algorithms (complex tree, linear discriminant, and K-nearest neighbor algorithms) with a maximum accuracy of 76.4%. Furthermore, bacterial differentiation was achieved on spiked samples of different species with different mixing ratios. The proposed ConvNet deep learning-assisted data analysis method of IFC exhibits advantages in analyzing a huge number of data sets with capacity for extracting predominant features within multicomponent information and will bring about progress and advances in the fields of both biosensing and data analysis.
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Affiliation(s)
- Shuaihua Zhang
- State Key Laboratory of Precision Measuring Technology & Instruments, College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, China
| | - Ziyu Han
- State Key Laboratory of Precision Measuring Technology & Instruments, College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, China
| | - Hang Qi
- State Key Laboratory of Precision Measuring Technology & Instruments, College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, China
| | - Siyuan Liu
- State Key Laboratory of Precision Measuring Technology & Instruments, College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, China
| | - Bohua Liu
- State Key Laboratory of Precision Measuring Technology & Instruments, College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, China
| | - Chongling Sun
- State Key Laboratory of Precision Measuring Technology & Instruments, College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, China
| | - Zhe Feng
- Wuqing District Center for Disease Control and Prevention, Tianjin 301700, China
| | - Meiqing Sun
- Wuqing District Center for Disease Control and Prevention, Tianjin 301700, China
| | - Xuexin Duan
- State Key Laboratory of Precision Measuring Technology & Instruments, College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, China
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14
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Desai JV, Lionakis MS. Evaluation of murine renal phagocyte-fungal interactions using intravital confocal microscopy and flow cytometry. STAR Protoc 2024; 5:102781. [PMID: 38113143 PMCID: PMC10770751 DOI: 10.1016/j.xpro.2023.102781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/31/2023] [Accepted: 12/01/2023] [Indexed: 12/21/2023] Open
Abstract
Myeloid phagocytes are essential for antifungal host defense during systemic candidiasis. Here, we present a protocol for assessing phagocyte-fungal interactions in vivo in the kidney, the primary target organ of the murine systemic candidiasis model. We describe steps for intravital confocal microscopy and flow cytometry. We also detail a kidney tissue dissociation procedure to obtain highly pure functional phagocytes for utilization in downstream ex vivo fungal uptake and killing assays.
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Affiliation(s)
- Jigar V Desai
- Fungal Pathogenesis Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Michail S Lionakis
- Fungal Pathogenesis Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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15
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Hu S, Zhang X, Yan W. Isolation and characterization of small extracellular vesicles from murine primary mammary tumor. STAR Protoc 2024; 5:102783. [PMID: 38103192 PMCID: PMC10770631 DOI: 10.1016/j.xpro.2023.102783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/29/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
Tumor-derived small extracellular vesicles (TEVs) play a pivotal role in cancer progression by transferring functional biomolecules between the parental and recipient cells. Here, we present a protocol to isolate TEVs directly from murine primary mammary tumor using differential centrifugation. We describe steps for tissue dissociation, enzymatic digestion, and centrifugation. We then detail procedures for characterization of TEVs through transmission electron microscopy, immunoblotting, and nano-flow cytometry. This protocol can be used to extract EVs from other solid tumor types. For complete details on the use and execution of this protocol, please refer to Li, Mei-Xin et al. (2023).1.
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Affiliation(s)
- Sheng Hu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaohui Zhang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China
| | - Wei Yan
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China.
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16
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Ausejo-Mauleon I, Labiano S, Alonso MM. Characterization of immune populations in the tumor microenvironment of diffuse midline glioma orthotopic mouse models by flow cytometry. STAR Protoc 2024; 5:102803. [PMID: 38159270 PMCID: PMC10805702 DOI: 10.1016/j.xpro.2023.102803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/24/2023] [Accepted: 12/13/2023] [Indexed: 01/03/2024] Open
Abstract
The immune response is a fundamental process in the treatment of solid tumors. Here, we present a protocol for implanting diffuse midline glioma cells in the brain of immune-competent mice and characterizing the different immune populations in the tumor microenvironment in a flow cytometry panel. We describe steps for processing of brain tumors, isolating the immune cells, and subsequent staining with antibodies for flow cytometry. We then detail procedures for implementing the gating strategy. For complete details on the use and execution of this protocol, please refer to Ausejo-Mauleon et al.1.
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Affiliation(s)
- Iker Ausejo-Mauleon
- Health Research Institute of Navarra (IdiSNA), Pamplona, Spain; Solid Tumor Program, CIMA-Universidad de Navarra, Pamplona, Spain; Department of Pediatrics, Clínica Universidad de Navarra, Pamplona, Spain
| | - Sara Labiano
- Health Research Institute of Navarra (IdiSNA), Pamplona, Spain; Solid Tumor Program, CIMA-Universidad de Navarra, Pamplona, Spain; Department of Pediatrics, Clínica Universidad de Navarra, Pamplona, Spain.
| | - Marta M Alonso
- Health Research Institute of Navarra (IdiSNA), Pamplona, Spain; Solid Tumor Program, CIMA-Universidad de Navarra, Pamplona, Spain; Department of Pediatrics, Clínica Universidad de Navarra, Pamplona, Spain.
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17
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Ma B, Zhou Y, Duan H, Sun Z, Han W, Qi H. Protocol to examine immune subpopulations in murine conjunctiva and lacrimal gland using flow cytometry. STAR Protoc 2024; 5:102921. [PMID: 38421865 PMCID: PMC10910354 DOI: 10.1016/j.xpro.2024.102921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 01/20/2024] [Accepted: 02/09/2024] [Indexed: 03/02/2024] Open
Abstract
Here, we present a protocol for the examination of immune cells in the murine conjunctiva and lacrimal gland using flow cytometry. We describe steps for dissection, preparation of high-quality single-cell suspensions, utilization of comprehensive staining panels, and optimization of flow cytometry voltage. We then detail procedures for compensation adjustments and the implementation of effective gating strategies. For complete details on the use and execution of this protocol, please refer to Ma et al.1.
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Affiliation(s)
- Baikai Ma
- Department of Ophthalmology, Peking University Third Hospital, Beijing 100191, China; Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing 100191, China.
| | - Yifan Zhou
- Department of Ophthalmology, Peking University Third Hospital, Beijing 100191, China; Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing 100191, China
| | - Hongyu Duan
- Department of Ophthalmology, Peking University Third Hospital, Beijing 100191, China; Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing 100191, China
| | - Zhengze Sun
- Department of Ophthalmology, Peking University Third Hospital, Beijing 100191, China; Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing 100191, China
| | - Wenling Han
- Department of Immunology, Peking University Health Science Center, Beijing 100083, China; NHC Key Laboratory of Medical Immunology, Peking University Health Science Center, Beijing 100083, China; Peking University Center for Human Disease Genomics, Beijing 100083, China.
| | - Hong Qi
- Department of Ophthalmology, Peking University Third Hospital, Beijing 100191, China; Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing 100191, China.
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18
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Gobbini A, Bandera A, Grifantini R, Abrignani S, Notarbartolo S. Protocol for the detection of defined T cell clones in a heterogeneous cell population. STAR Protoc 2024; 5:102787. [PMID: 38141168 PMCID: PMC10783555 DOI: 10.1016/j.xpro.2023.102787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/16/2023] [Accepted: 12/04/2023] [Indexed: 12/25/2023] Open
Abstract
Identifying defined T cell clones within a polyclonal population is key to clarifying their phenotype and function. Here, we present a protocol for detecting specified T cell clones in a heterogeneous cell population. We describe steps for stimulating human CD4+ T cells isolated from blood with a protein antigen, sorting antigen-specific cells by fluorescence-activated cell sorting, and detecting among these the presence of predefined T cell clones, based on their T cell receptor (TCR). TCR cDNA is amplified through 5'-RACE (TCR-SMART) and detected by qPCR. For complete details on the use and execution of this protocol, please refer to Notarbartolo et al. (2021).1.
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Affiliation(s)
- Andrea Gobbini
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", 20122 Milan, Italy
| | - Alessandra Bandera
- Infectious Diseases Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; Department of Pathophysiology and Transplantation, Università degli Studi di Milano, 20122 Milan, Italy; Centre for Multidisciplinary Research in Health Science (MACH), Università degli Studi di Milano, 20122 Milan, Italy
| | - Renata Grifantini
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", 20122 Milan, Italy; CheckmAb Srl, 20122 Milan, Italy
| | - Sergio Abrignani
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", 20122 Milan, Italy; Department of Clinical Sciences and Community Health, Università degli Studi di Milano, 20122 Milan, Italy
| | - Samuele Notarbartolo
- Infectious Diseases Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy.
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19
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Li Y, Liang Z, Wang H. Protocol for sorting and culturing of mouse early erythroid progenitor BFU-E cells. STAR Protoc 2024; 5:102718. [PMID: 38088932 PMCID: PMC10757283 DOI: 10.1016/j.xpro.2023.102718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/05/2023] [Accepted: 10/27/2023] [Indexed: 01/02/2024] Open
Abstract
Techniques allowing the long-term culture of the burst-forming unit of erythroid (BFU-E) progenitor cells are essential for understanding erythropoiesis. Here, we present a protocol for sorting mouse BFU-E cells and culturing them in a medium that promotes BFU-E cell expansion. We describe steps for isolating BFU-E cells from mouse fetal livers by combining magnetic microbeads with flow cytometry and culturing BFU-E cells with a specific expansion media. This approach can enhance the production of BFU-E cells. For complete details on the use and execution of this protocol, please refer to Li et al..1.
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Affiliation(s)
- Yao Li
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ziyu Liang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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20
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Magkouta S, Veroutis D, Pousias A, Papaspyropoulos A, Giannetti K, Pippa N, Lougiakis N, Kambas K, Lagopati N, Polyzou A, Georgiou M, Chountoulesi M, Pispas S, Foutadakis S, Kyrodimos E, Pouli N, Marakos P, Kotsinas A, Verginis P, Valakos D, Vatsellas G, Petty R, Thanos D, Demaria M, Evangelou K, Di Micco R, Gorgoulis VG. One-step rapid tracking and isolation of senescent cells in cellular systems, tissues, or animal models via GLF16. STAR Protoc 2024; 5:102929. [PMID: 38460134 PMCID: PMC10943059 DOI: 10.1016/j.xpro.2024.102929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/22/2024] [Accepted: 02/16/2024] [Indexed: 03/11/2024] Open
Abstract
Identification and isolation of senescent cells is challenging, rendering their detailed analysis an unmet need. We describe a precise one-step protocol to fluorescently label senescent cells, for flow cytometry and fluorescence microscopy, implementing a fluorophore-conjugated Sudan Black-B analog, GLF16. Also, a micelle-based approach allows identification of senescent cells in vivo and in vitro, enabling live-cell sorting for downstream analyses and live in vivo tracking. Our protocols are applicable to cellular systems, tissues, or animal models where senescence is present. For complete details on the use and execution of this protocol, please refer to Magkouta et al.1.
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Affiliation(s)
- Sophia Magkouta
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; Marianthi Simou and G.P. Livanos Labs, 1st Department of Critical Care and Pulmonary Services, School of Medicine, National & Kapodistrian University of Athens, ''Evangelismos'' Hospital, 10676 Athens, Greece
| | - Dimitris Veroutis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece
| | - Athanasios Pousias
- Department of Pharmacy, Division of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, 15771 Athens, Greece
| | - Angelos Papaspyropoulos
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece
| | - Kety Giannetti
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Natassa Pippa
- Section of Pharmaceutical Technology, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771 Athens, Greece; Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Nikolaos Lougiakis
- Department of Pharmacy, Division of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, 15771 Athens, Greece
| | | | - Nefeli Lagopati
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece; Laboratory of Biology, Department of Basic Medical Sciences, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Aikaterini Polyzou
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Maria Georgiou
- Department of Pharmacy, Division of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, 15771 Athens, Greece
| | - Maria Chountoulesi
- Section of Pharmaceutical Technology, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771 Athens, Greece
| | - Stergios Pispas
- Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 11635 Athens, Greece
| | - Spyros Foutadakis
- Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece
| | - Efthymios Kyrodimos
- First ENT Department, Hippocration Hospital, National Kapodistrian University of Athens, 11527 Athens, GR, Greece
| | - Nicole Pouli
- Department of Pharmacy, Division of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, 15771 Athens, Greece
| | - Panagiotis Marakos
- Department of Pharmacy, Division of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, 15771 Athens, Greece
| | - Athanassios Kotsinas
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Panayotis Verginis
- Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece; Laboratory of Immune Regulation and Tolerance, Division of Basic Sciences, University of Crete Medical School, 70013 Heraklion, Greece; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, 70013 Heraklion, Greece
| | - Dimitrios Valakos
- Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece
| | - Giannis Vatsellas
- Greek Genome Center, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece
| | - Russell Petty
- Ninewells Hospital and Medical School, University of Dundee, Dundee DD19SY, UK
| | - Dimitris Thanos
- Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece; Greek Genome Center, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece
| | - Marco Demaria
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, Groningen 9713 AV, The Netherlands
| | - Konstantinos Evangelou
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Raffaella Di Micco
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Vassilis G Gorgoulis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece; Ninewells Hospital and Medical School, University of Dundee, Dundee DD19SY, UK; Faculty Institute for Cancer Sciences, Manchester Academic Health Sciences Centre, University of Manchester, Manchester M20 4GJ, UK; Faculty of Health and Medical Sciences, University of Surrey, Surrey GU2 7YH, UK.
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21
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Amberg N, Cheung G, Hippenmeyer S. Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. STAR Protoc 2024; 5:102771. [PMID: 38070137 PMCID: PMC10755489 DOI: 10.1016/j.xpro.2023.102771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 10/09/2023] [Accepted: 11/22/2023] [Indexed: 01/01/2024] Open
Abstract
Mosaic analysis with double markers (MADM) technology enables the generation of genetic mosaic tissue in mice and high-resolution phenotyping at the individual cell level. Here, we present a protocol for isolating MADM-labeled cells with high yield for downstream molecular analyses using fluorescence-activated cell sorting (FACS). We describe steps for generating MADM-labeled mice, perfusion, single-cell suspension, and debris removal. We then detail procedures for cell sorting by FACS and downstream analysis. This protocol is suitable for embryonic to adult mice. For complete details on the use and execution of this protocol, please refer to Contreras et al. (2021).1.
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Affiliation(s)
- Nicole Amberg
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Giselle Cheung
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Simon Hippenmeyer
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria.
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22
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Mahony CB, Monteiro R. Protocol for the analysis of hematopoietic lineages in the whole kidney marrow of adult zebrafish. STAR Protoc 2024; 5:102810. [PMID: 38261517 PMCID: PMC10835462 DOI: 10.1016/j.xpro.2023.102810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/10/2023] [Accepted: 12/14/2023] [Indexed: 01/25/2024] Open
Abstract
The whole kidney marrow (WKM) is the site for hematopoiesis in the adult zebrafish. Here, we present a protocol for analyzing hematopoietic lineages in the WKM of adult zebrafish. We describe steps for the isolation of hematopoietic cells from the WKM, the downstream analysis of total marrow cellularity, and analysis of cell populations by flow cytometry. We then detail procedures for May-Grünwald-Giemsa staining for analysis of cellular morphology and phenotyping. For complete details on the use and execution of this protocol, please refer to Mahony et al.1.
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Affiliation(s)
- Christopher B Mahony
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
| | - Rui Monteiro
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
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23
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Tompa A, Faresjö M. Shift in the B cell subsets between children with type 1 diabetes and/or celiac disease. Clin Exp Immunol 2024; 216:36-44. [PMID: 38134245 DOI: 10.1093/cei/uxad136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 12/17/2023] [Indexed: 12/24/2023] Open
Abstract
Our purpose was to characterize the pattern of B cell subsets in children with a combined diagnosis of type 1 diabetes (T1D) and celiac disease (C) since children with single or double diagnosis of these autoimmune diseases may differ in peripheral B cell subset phenotype patterns. B cells were analyzed with flow cytometry for the expression of differentiation/maturation markers to identify transitional, naive, and memory B cells. Transitional (CD24hiCD38hiCD19+) and memory Bregs (mBregs; CD24hiCD27+CD19+, CD1d+CD27+CD19+, and CD5+CD1d+CD19+) were classified as B cells with regulatory capacity. Children with a combined diagnosis of T1D and C showed a pattern of diminished peripheral B cell subsets. The B cells compartment in children with combined diagnosis had higher percentages of memory B subsets and Bregs, including activated subsets, compared to children with either T1D or C. Children with combined diagnosis had a lower percentage of naive B cells (CD27-CD19+; IgD+CD19+) and an increased percentage of memory B cells (CD27+CD19+; IgD-CD19+). A similar alteration was seen among the CD39+ expressing naive and memory B cells. Memory Bregs (CD1d+CD27+CD19+) were more frequent, contrary to the lower percentage of CD5+ transitional Bregs in children with a combined diagnosis. In children with either T1D or C, the peripheral B cell compartment was dominated by naive cells. Differences in the pattern of heterogeneous peripheral B cell repertoire subsets reflect a shifting in the B cell compartment between children with T1D and/or C. This is an immunological challenge of impact on the pathophysiology of these autoimmune diseases.
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Affiliation(s)
- Andrea Tompa
- Department of Natural Science and Biomedicine, School of Health and Welfare, Jönköping University, Jönköping, Sweden
- Division of Diagnostics, Region Jönköping County, Jönköping, Sweden
| | - Maria Faresjö
- Department of Natural Science and Biomedicine, School of Health and Welfare, Jönköping University, Jönköping, Sweden
- Department of Life Sciences, Division of Systems and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden
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Bushell D, Tan JKH, Smith J, Moro C. The identification of diurnal variations on circulating immune cells by finger prick blood sampling in small sample sizes: a pilot study. Lab Med 2024; 55:220-226. [PMID: 37478465 PMCID: PMC10920974 DOI: 10.1093/labmed/lmad062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2023] Open
Abstract
OBJECTIVE There are well-described impacts of biological rhythms on human physiology. With the increasing push for routine blood tests for preventative medical care and clinical and physiological research, optimizing effectiveness is paramount. This study aimed to determine whether it is feasible to assess diurnal variations of peripheral lymphocyte prevalence using finger prick blood in a small sample size. METHODS Using polychromatic flow cytometry, the prevalence of lymphocytes was assessed using 25 µL fingertip blood samples at 8 AM and 5 PM from 8 participants. RESULTS TH cells and B cells showed significantly higher percentages in the 5 PM samples, whereas NK cells demonstrated a significantly higher morning percentage. T cells, leukocytes, and cytotoxic T cells showed no significant changes. CONCLUSION The detection of diurnal variations demonstrates that small blood volumes can be used to detect lymphocyte variations. The lower blood volume required provides a new testing method for clinical and research settings.
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Affiliation(s)
- Dayna Bushell
- Faculty of Health Sciences and Medicine, Bond University, Robina, Australia
| | | | - Jessica Smith
- Clem Jones Centre for Regenerative Medicine, Bond University, Robina, Australia
| | - Christian Moro
- Faculty of Health Sciences and Medicine, Bond University, Robina, Australia
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25
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Hua X, Han K, Mandracchia B, Radmand A, Liu W, Kim H, Yuan Z, Ehrlich SM, Li K, Zheng C, Son J, Silva Trenkle AD, Kwong GA, Zhu C, Dahlman JE, Jia S. Light-field flow cytometry for high-resolution, volumetric and multiparametric 3D single-cell analysis. Nat Commun 2024; 15:1975. [PMID: 38438356 PMCID: PMC10912605 DOI: 10.1038/s41467-024-46250-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 02/15/2024] [Indexed: 03/06/2024] Open
Abstract
Imaging flow cytometry (IFC) combines flow cytometry and fluorescence microscopy to enable high-throughput, multiparametric single-cell analysis with rich spatial details. However, current IFC techniques remain limited in their ability to reveal subcellular information with a high 3D resolution, throughput, sensitivity, and instrumental simplicity. In this study, we introduce a light-field flow cytometer (LFC), an IFC system capable of high-content, single-shot, and multi-color acquisition of up to 5,750 cells per second with a near-diffraction-limited resolution of 400-600 nm in all three dimensions. The LFC system integrates optical, microfluidic, and computational strategies to facilitate the volumetric visualization of various 3D subcellular characteristics through convenient access to commonly used epi-fluorescence platforms. We demonstrate the effectiveness of LFC in assaying, analyzing, and enumerating intricate subcellular morphology, function, and heterogeneity using various phantoms and biological specimens. The advancement offered by the LFC system presents a promising methodological pathway for broad cell biological and translational discoveries, with the potential for widespread adoption in biomedical research.
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Affiliation(s)
- Xuanwen Hua
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Keyi Han
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Biagio Mandracchia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Afsane Radmand
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Chemical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Wenhao Liu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Hyejin Kim
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Zhou Yuan
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
- Georgia W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Samuel M Ehrlich
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
- Georgia W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kaitao Li
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Corey Zheng
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Jeonghwan Son
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Aaron D Silva Trenkle
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Gabriel A Kwong
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Cheng Zhu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - James E Dahlman
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Shu Jia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA.
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26
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Eich C, Vogt JF, Längst V, Clausen BE, Hövelmeyer N. Isolation and high-dimensional flow cytometric analysis of tumor-infiltrating leukocytes in a mouse model of colorectal cancer. Front Immunol 2024; 15:1295863. [PMID: 38500875 PMCID: PMC10944955 DOI: 10.3389/fimmu.2024.1295863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 02/09/2024] [Indexed: 03/20/2024] Open
Abstract
Colorectal cancer (CRC) is a complex and heterogeneous disease characterized by dysregulated interactions between tumor cells and the immune system. The tumor microenvironment plays a pivotal role in cancer initiation as well as progression, with myeloid immune cells such as dendritic cell and macrophage subsets playing diverse roles in cancer immunity. On one hand, they exert anti-tumor effects, but they can also contribute to tumor growth. The AOM/DSS colitis-associated cancer mouse model has emerged as a valuable tool to investigate inflammation-driven CRC. To understand the role of different leukocyte populations in tumor development, the preparation of single cell suspensions from tumors has become standard procedure for many types of cancer in recent years. However, in the case of AOM/DSS-induced colorectal tumors, this is still challenging and rarely described. For one, to be able to properly distinguish tumor-associated immune cells, separate processing of cancerous and surrounding colon tissue is essential. In addition, cell yield, due to the low tumor mass, viability, as well as preservation of cell surface epitopes are important for successful flow cytometric profiling of tumor-infiltrating leukocytes. Here we present a fast, simple, and economical step-by-step protocol for isolating colorectal tumor-associated leukocytes from AOM/DSS-treated mice. Furthermore, we demonstrate the feasibility of this protocol for high-dimensional flow cytometric identification of the different tumor-infiltrating leukocyte populations, with a specific focus on myeloid cell subsets.
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Affiliation(s)
- Christina Eich
- Institute for Molecular Medicine, Paul Klein Center for Immune Intervention, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Johannes F. Vogt
- Institute for Molecular Medicine, Paul Klein Center for Immune Intervention, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Vivian Längst
- Institute for Molecular Medicine, Paul Klein Center for Immune Intervention, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Björn E. Clausen
- Institute for Molecular Medicine, Paul Klein Center for Immune Intervention, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Nadine Hövelmeyer
- Institute for Molecular Medicine, Paul Klein Center for Immune Intervention, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
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27
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Imbratta C, Reid T, Toefy A, Scriba TJ, Nemes E. OMIP-101: 27-color flow cytometry panel for immunophenotyping of major leukocyte populations in fixed whole blood. Cytometry A 2024; 105:165-170. [PMID: 38343094 PMCID: PMC10958279 DOI: 10.1002/cyto.a.24827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 01/12/2024] [Accepted: 01/24/2024] [Indexed: 03/16/2024]
Abstract
This 27-color flow cytometry antibody panel allows broad immune-profiling of major leukocyte subsets in human whole blood (WB). It includes lineage markers to identify myeloid and lymphoid cell populations including granulocytes, monocytes, myeloid dendritic cells (mDCs), natural killer (NK) cells, NKT-like cells, B cells, conventional CD4 and CD8 T cells, γδ T cells, mucosa-associated invariant T (MAIT) cells and innate lymphoid cells (ILC). To further characterize each of these populations, markers defining stages of cell differentiation (CCR7, CD27, CD45RA, CD127, CD57), cytotoxic potential (perforin, granzyme B) and cell activation/proliferation (HLA-DR, CD38, Ki-67) were included. This panel was developed for quantifying absolute counts and phenotyping major leukocyte populations in cryopreserved, fixed WB collected from participants enrolled in large multi-site tuberculosis (TB) vaccine clinical trials. This antibody panel can be applied to profile major leukocyte subsets in other sample types such as fresh WB or peripheral blood mononuclear cells (PBMCs) with only minor additional optimization.
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Affiliation(s)
- Claire Imbratta
- South African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Tim Reid
- South African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Asma Toefy
- South African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Thomas J. Scriba
- South African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Elisa Nemes
- South African Tuberculosis Vaccine Initiative, Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
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28
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Ramirez NJ, Schulze JJ, Walter S, Werner J, Mrovecova P, Olek S, Sachsenmaier C, Grimbacher B, Salzer U. Epigenetic immune cell quantification for diagnostic evaluation and monitoring of patients with inborn errors of immunity and secondary immune deficiencies. Clin Immunol 2024; 260:109920. [PMID: 38307474 DOI: 10.1016/j.clim.2024.109920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/04/2024]
Abstract
BACKGROUND Early detection and monitoring of primary immunodeficiencies (PID) in humans require quantitative determination of immune cells from fresh blood analyzed by flow cytometry. However, epigenetic immune cell quantification allows analysis from fresh, frozen, or dried blood samples. We demonstrate the utility of epigenetic immune cell quantification for patients with PID. METHODS Epigenetic quantification of basic lymphocyte subpopulations of 259 samples from PID patients were compared to flow cytometric data. Epigenetic analysis was extended to T-cell subsets (Treg, Th17, Tfh, PD-1+, CCR6+) and memory B-cells and compared between venous EDTA and dried blood. RESULTS A high correlation of >0.9 was observed for basic T- and B-cell subsets. Extended epigenetic analysis showed quantitative trends within PID subgroups, but individually these varied substantially within these groups. Epigenetic analysis of dried blood samples was equivalent to EDTA blood. CONCLUSION Epigenetic immune cell quantification is suitable for immune cell profiling in PID patients.
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Affiliation(s)
- Neftali J Ramirez
- Institute for Immunodeficiency, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | | | | | - Pavla Mrovecova
- Institute for Immunodeficiency, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sven Olek
- Ivana Turbachova Laboratory for Epigenetics, Precision for Medicine GmbH, Berlin, Germany
| | | | - Bodo Grimbacher
- Institute for Immunodeficiency, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Clinic of Rheumatology and Clinical Immunology, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany; DZIF - German Center for Infection Research, Satellite Center Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University, Freiburg, Germany; RESIST - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Germany.
| | - Ulrich Salzer
- Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Clinic of Rheumatology and Clinical Immunology, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany.
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29
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Maurer-Granofszky M, Kohrer S, Fischer S, Schumich A, Nebral K, Larghero P, Meyer C, Mecklenbrauker A, Muhlegger N, Marschalek R, Haas OA, Panzer-Grumayer R, Dworzak MN. Genomic breakpoint-specific monitoring of measurable residual disease in pediatric non-standard-risk acute myeloid leukemia. Haematologica 2024; 109:740-750. [PMID: 37345487 PMCID: PMC10910191 DOI: 10.3324/haematol.2022.282424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 06/15/2023] [Indexed: 06/23/2023] Open
Abstract
Pediatric acute myeloid leukemia (AML) is a highly heterogeneous disease making standardized measurable residual disease (MRD) assessment challenging. Currently, patient-specific DNA-based assays are only rarely applied for MRD assessment in pediatric AML. We tested whether quantification of genomic breakpoint-specific sequences via quantitative polymerase chain reaction (gDNA-PCR) provides a reliable means of MRD quantification in children with non-standardrisk AML and compared its results to those obtained with state-of-the-art ten-color flow cytometry (FCM). Breakpointspecific gDNA-PCR assays were established according to Euro-MRD consortium guidelines. FCM-MRD assessment was performed according to the European Leukemia Network guidelines with adaptations for pediatric AML. Of 77 consecutively recruited non-standard-risk pediatric AML cases, 49 (64%) carried a chromosomal translocation potentially suitable for MRD quantification. Genomic breakpoint analysis returned a specific DNA sequence in 100% (41/41) of the cases submitted for investigation. MRD levels were evaluated using gDNA-PCR in 243 follow-up samples from 36 patients, achieving a quantitative range of at least 10-4 in 231/243 (95%) of samples. Comparing gDNA-PCR with FCM-MRD data for 183 bone marrow follow-up samples at various therapy timepoints showed a high concordance of 90.2%, considering a cut-off of ≥0.1%. Both methodologies outperformed morphological assessment. We conclude that MRD monitoring by gDNA-PCR is feasible in pediatric AML with traceable genetic rearrangements and correlates well with FCM-MRD in the currently applied clinically relevant range, while being more sensitive below that. The methodology should be evaluated in larger cohorts to pave the way for clinical application.
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Affiliation(s)
| | - Stefan Kohrer
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; Labdia Labordiagnostik, Vienna
| | - Susanna Fischer
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; Labdia Labordiagnostik, Vienna
| | - Angela Schumich
- St. Anna Children's Cancer Research Institute (CCRI), Vienna
| | - Karin Nebral
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; Labdia Labordiagnostik, Vienna
| | - Patrizia Larghero
- Institute of Pharmaceutical Biology/Diagnostic Center of Acute Leukemia (DCAL), Goethe-University, Frankfurt/Main
| | - Claus Meyer
- Institute of Pharmaceutical Biology/Diagnostic Center of Acute Leukemia (DCAL), Goethe-University, Frankfurt/Main
| | - Astrid Mecklenbrauker
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; Labdia Labordiagnostik, Vienna
| | - Nora Muhlegger
- St. Anna Children's Cancer Research Institute (CCRI), Vienna
| | - Rolf Marschalek
- Institute of Pharmaceutical Biology/Diagnostic Center of Acute Leukemia (DCAL), Goethe-University, Frankfurt/Main
| | - Oskar A Haas
- St. Anna Children's Cancer Research Institute (CCRI), Vienna
| | | | - Michael N Dworzak
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; Labdia Labordiagnostik, Vienna, Austria; St. Anna Children's Hospital, Department of Pediatrics, Medical University of Vienna, Vienna.
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Co Soriano JC, Tsutsumi S, Ohara D, Hirota K, Kondoh G, Niwa T, Taguchi H, Kadonosono T, Kizaka-Kondoh S. Identification of Surface Markers and Functional Characterization of Myeloid Derived Suppressor Cell-Like Adherent Cells. Adv Biol (Weinh) 2024; 8:e2300159. [PMID: 37986133 DOI: 10.1002/adbi.202300159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 10/11/2023] [Indexed: 11/22/2023]
Abstract
Myeloid-derived suppressor cell (MDSC)-like adherent cells (MLACs) are a recently identified CD11b+ F4/80- myeloid cell subset that can infiltrate tumors early in development and promote their growth. Because of these functions, MLACs play an important role in establishing an immunosuppressive tumor microenvironment (TME). However, the lack of MLAC-specific markers has hampered further characterization of this cell type. This study identifies the gene signature of MLACs by analyzing RNA-sequencing (RNA-seq) and public single-cell RNA-seq data, revealing that MLACs are an independent cell population that are distinct from other intratumoral myeloid cells. After combining proteome analysis of membrane proteins with RNA-seq data, H2-Ab1 and CD11c are indicated as marker proteins that can support the isolation of MLAC subsets from CD11b+ F4/80- myeloid cells by fluorescence-activated cell sorting. The CD11b+ F4/80- H2-Ab1+ and CD11b+ F4/80- CD11c+ MLAC subsets represent approximately half of the MLAC population that is isolated based on their adhesion properties and possess gene signatures and functional properties similar to those of the MLAC population. Additionally, membrane proteome analysis suggests that MLACs express highly heterogeneous surface proteins. This study facilitates an integrated understanding of heterogeneous intratumoral myeloid cells, as well as the molecular and cellular details of the development of an immunosuppressive TME.
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Affiliation(s)
- John Clyde Co Soriano
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Shiho Tsutsumi
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Daiya Ohara
- Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo-Ku, Kyoto, 606-8507, Japan
| | - Keiji Hirota
- Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo-Ku, Kyoto, 606-8507, Japan
| | - Gen Kondoh
- Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo-Ku, Kyoto, 606-8507, Japan
| | - Tatsuya Niwa
- Institute for Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
| | - Hideki Taguchi
- Institute for Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
| | - Tetsuya Kadonosono
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Shinae Kizaka-Kondoh
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
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31
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Ashouri K, Nittur V, Ginosyan AA, Hwang J, Adnani B, Chen D, Savitala-Damerla L, Schiff K, Chaudhary P, Kovach AE, Ladha A, Siddiqi I, Ali A, Woan K, Tam E, Yaghmour G. Concordance of Next-Generation Sequencing and Multiparametric Flow Cytometry Methods for Detecting Measurable Residual Disease in Adult Acute Lymphoblastic Leukemia: Optimizing Prediction of Clinical Outcomes From a Single-Center Study. Clin Lymphoma Myeloma Leuk 2024; 24:e59-e66.e2. [PMID: 38061959 DOI: 10.1016/j.clml.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/14/2023] [Accepted: 11/14/2023] [Indexed: 03/01/2024]
Abstract
INTRODUCTION Detection of measurable residual disease (MRD) in adults with acute lymphoblastic leukemia (ALL) is a vital biomarker in risk prediction and treatment selection. Next-generation sequencing (NGS) offers greater sensitivity relative to multiparametric flow cytometry (MFC) and may be a better predictive tool for identifying ALL patients at risk of relapse. PATIENTS AND METHODS This single-center retrospective study compares MRD detection by NGS versus MFC in 52 adult B- and T-ALL patients treated at our institution between 2018 and 2023. Pretreatment bone marrow samples were used for assay calibration, while post-treatment MRD assessment was completed up to 4.5 months after the first complete remission (CR1) using an MRD cutoff of 10-6 for distinguishing relapse risk. RESULTS The 2-year cumulative incidence of relapse (CIR) among patients who were MRD positive using MFC and NGS was 39.5% and 46.2%, respectively. Unlike MFC, post-CR1 MRD positivity with NGS significantly predicted CIR (HR = 9.47, P = .028). In patients who were MRD negative by MFC, low levels of MRD detected by NGS distinguished patients at high risk of relapse (HR 10.3, P = .026, 2-year CIR 51.6%). CONCLUSION Our data suggests that assessment of post-CR1 MRD using a highly sensitive NGS assay can identify ALL patients undergoing frontline therapy at increased risk of relapse and guide the use of adjuvant therapy.
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Affiliation(s)
- Karam Ashouri
- Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Vinay Nittur
- Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Anush A Ginosyan
- Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Jennifer Hwang
- Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Blake Adnani
- Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Denaly Chen
- Jane Anne Nohl Division of Hematology and Center for the study of Blood disease, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Lakshmi Savitala-Damerla
- Jane Anne Nohl Division of Hematology and Center for the study of Blood disease, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Kimberly Schiff
- Jane Anne Nohl Division of Hematology and Center for the study of Blood disease, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Preet Chaudhary
- Jane Anne Nohl Division of Hematology and Center for the study of Blood disease, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Alexandra E Kovach
- Keck School of Medicine, University of Southern California, Los Angeles, CA; Hematopathology, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA
| | - Abdullah Ladha
- Jane Anne Nohl Division of Hematology and Center for the study of Blood disease, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Imran Siddiqi
- Keck School of Medicine, University of Southern California, Los Angeles, CA; Division of Pathology, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Amir Ali
- Department of Pharmacy, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Karrune Woan
- Jane Anne Nohl Division of Hematology and Center for the study of Blood disease, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Eric Tam
- Jane Anne Nohl Division of Hematology and Center for the study of Blood disease, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA
| | - George Yaghmour
- Jane Anne Nohl Division of Hematology and Center for the study of Blood disease, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA.
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Marder G, Quach T, Chadha P, Nandkumar P, Tsang J, Levine T, Schiopu E, Furie R, Davidson A, Narain S. Belimumab treatment of adult idiopathic inflammatory myopathy. Rheumatology (Oxford) 2024; 63:742-750. [PMID: 37326854 PMCID: PMC10907809 DOI: 10.1093/rheumatology/kead281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/16/2023] [Accepted: 05/31/2023] [Indexed: 06/17/2023] Open
Abstract
OBJECTIVE To evaluate belimumab addition to the standard of care in patents with refractory idiopathic inflammatory myopathy (IIM). METHODS We conducted a 40-week multicentre, randomized, double-blind, placebo-controlled trial with 1:1 IV belimumab 10 mg/kg or placebo randomization and a 24-week open-label extension. Clinical responses were measured by the definition of improvement (DOI) and total improvement score (TIS). Flow cytometry analyses were performed on available samples before randomization, at 24 and 60-64 weeks. Descriptive statistics, t-test, Fisher's exact test and analysis of variance tests were used. RESULTS A total of 17 patients were randomized, 15 received five or more doses of belimumab or placebo and were included in the intention-to-treat analysis. More belimumab patients vs placebo attained a TIS ≥40 [55.5% vs 33.3%; P = non-significant (NS)] and achieved the DOI (33.3% vs 16.7%; P = NS) at weeks 40 and 64; the mean TIS was similar among groups. Two patients achieved major responses (TIS = 72.5) after week 40 in the belimumab arm and none in the placebo arm. No improvement in the placebo arm after switching to the open-label phase was observed. There was no steroid-sparing effect. No new safety signals were detected. Although total B cells were not reduced, belimumab induced naïve B cell depletion while enhancing the number and frequency memory B cells. CONCLUSION The study did not meet the primary endpoint and no statistically significant differences were observed in clinical responses between arms. More patients achieved sustained TIS ≥40 and reached the DOI. Most patients who received belimumab for >40 weeks had clinical improvement. Phenotypic changes in B cell populations were not associated with clinical responses. CLINICAL TRIAL REGISTRATION NUMBER Clinicaltrials.gov (https://clinicaltrials.gov/), NCT02347891.
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Affiliation(s)
- Galina Marder
- Division of Rheumatology, Northwell Health, Donald and Barbara Zucker School of Medicine, Great Neck, NY, USA
| | - Tam Quach
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Priyal Chadha
- Division of Rheumatology, Northwell Health, Donald and Barbara Zucker School of Medicine, Great Neck, NY, USA
| | - Preeya Nandkumar
- Division of Rheumatology, Northwell Health, Donald and Barbara Zucker School of Medicine, Great Neck, NY, USA
| | - Jimmy Tsang
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Todd Levine
- Phoenix Neurological Associates, Phoenix, AZ, USA
| | - Elena Schiopu
- Division of Rheumatology, University of Michigan, Ann Arbor, MI, USA
| | - Richard Furie
- Division of Rheumatology, Northwell Health, Donald and Barbara Zucker School of Medicine, Great Neck, NY, USA
| | - Anne Davidson
- Division of Rheumatology, Northwell Health, Donald and Barbara Zucker School of Medicine, Great Neck, NY, USA
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Sonali Narain
- Division of Rheumatology, Northwell Health, Donald and Barbara Zucker School of Medicine, Great Neck, NY, USA
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Cox AM, Kim D, García R, Fuda FS, Weinberg OK, Chen W. Automated prediction of acute promyelocytic leukemia from flow cytometry data using a graph neural network pipeline. Am J Clin Pathol 2024; 161:264-272. [PMID: 37878540 DOI: 10.1093/ajcp/aqad145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/22/2023] [Indexed: 10/27/2023] Open
Abstract
OBJECTIVES Our study aimed to develop a machine learning (ML) model to accurately classify acute promyelocytic leukemia (APL) from other types of acute myeloid leukemia (other AML) using multicolor flow cytometry (MFC) data. Multicolor flow cytometry is used to determine immunophenotypes that serve as disease signatures for diagnosis. METHODS We used a data set of MFC files from 27 patients with APL and 41 patients with other AML, including those with uncommon immunophenotypes. Our ML pipeline involved training a graph neural network (GNN) to output graph-level labels and identifying the most crucial MFC parameters and cells for predictions using an input perturbation method. RESULTS The top-performing GNN achieved 100% accuracy on the training/validation and test sets on classifying APL from other AML and used MFC parameters similarly to expert pathologists. Pipeline performance is amenable to use in a clinical decision support system, and our deep learning architecture readily enables prediction explanations. CONCLUSIONS Our ML pipeline shows robust performance on predicting APL and could be used to screen for APL using MFC data. It also allowed for intuitive interrogation of the model's predictions by clinicians.
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Affiliation(s)
- Andrew M Cox
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, US
| | - Daehwan Kim
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, US
| | - Rolando García
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, US
| | - Franklin S Fuda
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, US
| | - Olga K Weinberg
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, US
| | - Weina Chen
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, US
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Zhu Y, Li L, Wang Z, Tan X, Tao J, Ding L, Dong H, Ye P. [IL-1β inhibits macrophage M2 polarization by down-regulating CD200 expression in human umbilical cord mesenchymal stem cells]. Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi 2024; 40:193-198. [PMID: 38512028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Objective To investigate the regulation of IL-1β on the expression of CD200 in human umbilical cord mesenchymal stem cells (hUC-MSCs), its role in macrophage polarization and the underlying mechanism. Methods hUC-MSCs were isolated and cultured in serum-free medium. Morphological observation and the expressions of CD73, CD90, CD105, CD14, CD34, CD45 and HLA-DR were detected by flow cytometry to confirm the properties of mesenchymal stem cells. hUC-MSCs were treated with IL-1β at the final concentration of 20 ng/mL for 24 hours. The proportion of CD200 positive cells was measured by flow cytometry. Real-time quantitative PCR and Western blot analysis were used to detect CD200 mRNA and protein expression levels. hUC-MSCs infected with CD200 overexpression (OE-CD200) and its negative control (OE-NC) lectin virus were treated with IL-1β and co-cultured with PMA-activated THP-1 macrophages. The proportion of CD11c and CD206 positive cells was measured by flow cytometry. hUC-MSCs were treated with IL-1β in combination with PD98059, and the expression of MAPK signaling pathway-related proteins and its effect on CD200 expression were detected by Western blot analysis. Results IL-1β significantly down-regulated the expression of CD200 protein and the proportion of CD200 positive cells. Overexpression of CD200 significantly up-regulated the expression of CD200 in hUC-MSCs, and increased the proportion of CD206-positive macrophages. IL-1β activated the ERK1/2 signaling pathway in hUC-MSCs, and PD98059 up-regulated the expression of CD200 protein in hUC-MSCs treated with IL-1β. Conclusion IL-1β inhibits the expression of CD200 by activating ERK1/2 signaling pathway, and reduces the immunosuppressive effect of hUC-MSCs on regulating the M2-type polarization of macrophages.
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Affiliation(s)
- Yongzhao Zhu
- Institute of Medical Sciences, General Hospital of Ningxia Medical University, Yinchuan 750004, China
| | - Li Li
- Institute of Medical Sciences, General Hospital of Ningxia Medical University, Yinchuan 750004, China
| | - Zheng Wang
- Institute of Medical Sciences, General Hospital of Ningxia Medical University, Yinchuan 750004, China
| | - Xipeng Tan
- Institute of Medical Sciences, General Hospital of Ningxia Medical University, Yinchuan 750004, China
| | - Jin Tao
- Institute of Medical Sciences, General Hospital of Ningxia Medical University, Yinchuan 750004, China
| | - Lu Ding
- Institute of Medical Sciences, General Hospital of Ningxia Medical University, Yinchuan 750004, China
| | - Hui Dong
- Institute of Medical Sciences, General Hospital of Ningxia Medical University, Yinchuan 750004, China
| | - Peng Ye
- Institute of Medical Sciences, General Hospital of Ningxia Medical University, Yinchuan 750004, China. *Corresponding author, E-mail:
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Patel VJ, Joharapurkar A, Jain MR. The Perspective of Using Flow Cytometry for Unpuzzling Hypoxia-Inducible Factors Signalling. Drug Res (Stuttg) 2024; 74:113-122. [PMID: 38350634 DOI: 10.1055/a-2248-9180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
Hypoxia-inducible factors (HIFs) are transcription factors that are responsible for adapting to the changes in oxygen levels in the cellular environment. HIF activity determines the expression of cellular proteins that control the development and physiology of the cells and pathophysiology of a disease. Understanding the role of specific HIF (HIF-1-3) in cellular function is essential for development of the HIF-targeted therapies. In this review, we have discussed the use of flow cytometry in analysing HIF function in cells. Proper understanding of HIF-signalling will help to design pharmacological interventions HIF-mediated therapy. We have discussed the role of HIF-signalling in various diseases such as cancer, renal and liver diseases, ulcerative colitis, arthritis, diabetes and diabetic complications, psoriasis, and wound healing. We have also discussed protocols that help to decipher the role of HIFs in these diseases that would eventually help to design promising therapies.
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Affiliation(s)
- Vishal J Patel
- Department of Pharmacology and Toxicology, Zydus Research Centre, Zydus Lifesciences Limited, Moraiya, Ahmedabad, India
| | - Amit Joharapurkar
- Department of Pharmacology and Toxicology, Zydus Research Centre, Zydus Lifesciences Limited, Moraiya, Ahmedabad, India
| | - Mukul R Jain
- Department of Pharmacology and Toxicology, Zydus Research Centre, Zydus Lifesciences Limited, Moraiya, Ahmedabad, India
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Rodzinski É, Martin N, Rouget R, Pioger A, Dehennaut V, Molendi-Coste O, Dombrowicz D, Goy E, de Launoit Y, Abbadie C. [Sorting of senescent cells by flow cytometry: Specificities and pitfalls to avoid]. Med Sci (Paris) 2024; 40:275-282. [PMID: 38520103 DOI: 10.1051/medsci/2024011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2024] Open
Abstract
Cells can be reprogrammed into senescence to adapt to a variety of stresses, most often affecting the genome integrity. Senescent cells accumulate with age or upon various insults in almost all tissues, and contribute to the development of several age-associated pathologies. Studying the molecular pathways involved in senescence induction, maintenance, or escape is challenged by the heterogeneity in the level of commitment to senescence, and by the pollution of senescent cell populations by proliferating pre- or post-senescent cells. We coped with these difficulties by developing a protocol for sorting senescent cells by flow cytometry, based on three major senescence markers : the SA-β-Galactosidase activity, the size of the cells, and their granularity reflecting the accumulation of aggregates, lysosomes, and altered mitochondria. We address the issues related to sorting senescent cells, the pitfalls to avoid, and propose solutions for sorting viable cells expressing senescent markers at different extents.
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Affiliation(s)
- Élodie Rodzinski
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277 - CANTHER (Cancer Heterogeneity Plasticity and Resistance to Therapies), F-59000 Lille, France
| | - Nathalie Martin
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277 - CANTHER (Cancer Heterogeneity Plasticity and Resistance to Therapies), F-59000 Lille, France
| | - Raphael Rouget
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277 - CANTHER (Cancer Heterogeneity Plasticity and Resistance to Therapies), F-59000 Lille, France
| | - Adrien Pioger
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277 - CANTHER (Cancer Heterogeneity Plasticity and Resistance to Therapies), F-59000 Lille, France
| | - Vanessa Dehennaut
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277 - CANTHER (Cancer Heterogeneity Plasticity and Resistance to Therapies), F-59000 Lille, France
| | - Olivier Molendi-Coste
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US41 - UAR 2014 - PLBS, F-59000 Lille, France
| | - David Dombrowicz
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011 - EGID, F-59000 Lille, France
| | - Erwan Goy
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277 - CANTHER (Cancer Heterogeneity Plasticity and Resistance to Therapies), F-59000 Lille, France
| | - Yvan de Launoit
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277 - CANTHER (Cancer Heterogeneity Plasticity and Resistance to Therapies), F-59000 Lille, France
| | - Corinne Abbadie
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277 - CANTHER (Cancer Heterogeneity Plasticity and Resistance to Therapies), F-59000 Lille, France
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Jyoti TP, Chandel S, Singh R. Flow cytometry: Aspects and application in plant and biological science. J Biophotonics 2024; 17:e202300423. [PMID: 38010848 DOI: 10.1002/jbio.202300423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 10/28/2023] [Indexed: 11/29/2023]
Abstract
Flow cytometry is a potent method that enables the quick and concurrent investigation of several characteristics of single cells in solution. Photodiodes or photomultiplier tubes are employed to detect the dispersed and fluorescent light signals that are produced by the laser beam as it passes through the cells. Photodetectors transform the light signals produced by the laser into electrical impulses. A computer then analyses these electrical impulses to identify and measure the various cell populations depending on their fluorescence or light scattering characteristics. Based on their fluorescence or light scattering properties, cell populations can be examined and/or isolated. This review covers the basic principle, components, working and specific biological applications of flow cytometry, including studies on plant, cell and molecular biology and methods employed for data processing and interpretation as well as the potential future relevance of this methodology in light of retrospective analysis and recent advancements in flow cytometry.
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Affiliation(s)
- Thakur Prava Jyoti
- Department of Pharmacognosy, ISF College of Pharmacy, Moga, Punjab, India
| | - Shivani Chandel
- Department of Pharmacognosy, ISF College of Pharmacy, Moga, Punjab, India
| | - Rajveer Singh
- Department of Pharmacognosy, ISF College of Pharmacy, Moga, Punjab, India
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Luah YH, Wu T, Cheow LF. Identification, sorting and profiling of functional killer cells via the capture of fluorescent target-cell lysate. Nat Biomed Eng 2024; 8:248-262. [PMID: 37652987 DOI: 10.1038/s41551-023-01089-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/04/2023] [Indexed: 09/02/2023]
Abstract
Assays for assessing cell-mediated cytotoxicity are largely target-cell-centric and cannot identify and isolate subpopulations of cytotoxic effector cells. Here we describe an assay compatible with flow cytometry for the accurate identification and sorting of functional killer-cell subpopulations in co-cultures. The assay, which we named PAINTKiller (for 'proximity affinity intracellular transfer identification of killer cells'), relies on the detection of an intracellular fluorescent protein 'painted' by a lysed cell on the surface of the lysing cytotoxic cell (specifically, on cell lysis the intracellular fluorescein derivative carboxyfluorescein succinimidyl ester is captured on the surface of the natural killer cell by an antibody for anti-fluorescein isothiocyanate linked to an antibody for the pan-leucocyte surface receptor CD45). The assay can be integrated with single-cell RNA sequencing for the analysis of molecular pathways associated with cell cytotoxicity and may be used to uncover correlates of functional immune responses.
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Affiliation(s)
- Yen Hoon Luah
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
- Critical Analytics for Manufacturing of Personalized-Medicine Interdisciplinary Research Group, Singapore-MIT Alliance in Research and Technology, Singapore, Singapore
| | - Tongjin Wu
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
| | - Lih Feng Cheow
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore.
- Critical Analytics for Manufacturing of Personalized-Medicine Interdisciplinary Research Group, Singapore-MIT Alliance in Research and Technology, Singapore, Singapore.
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore.
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Battais F, Langonné I, Muller S, Mathiot J, Coiscaud A, Audry A, Remy AM, Sponne I, Mourot-Bousquenaud M. The BMDC model, a performant cell-based test to assess the sensitizing potential and potency of chemicals including pre/pro-haptens. Contact Dermatitis 2024; 90:211-234. [PMID: 37852624 DOI: 10.1111/cod.14439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 09/07/2023] [Accepted: 10/01/2023] [Indexed: 10/20/2023]
Abstract
BACKGROUND Chemical-induced allergies at workplace represent a significant occupational health issue. These substances must be properly identified as sensitizers. In previous studies, an original model using mouse bone marrow-derived dendritic cells (BMDC) was developed for this purpose. OBJECTIVES The aim of this study was to evaluate the predictive capacity of the BMDC model with a large panel of sensitizers (including pre- and pro-haptens) and non-sensitizers. METHODS The readout from the BMDC model is based on expression levels of six phenotypic markers measured by flow cytometry. RESULTS The results indicate that 29 of the 37 non-sensitizers, and 81 of the 86 sensitizers were correctly classified compared to the Local Lymph Node Assay (LLNA). Statistical analysis revealed the BMDC model to have a sensitivity of 94%, a specificity of 78%, and an accuracy of 89%. The EC2 (Effective Concentration) values calculated with this model allow sensitizers to be categorized into four classes: extreme, strong, moderate and weak. CONCLUSIONS These excellent predictive performances show that the BMDC model discriminates between sensitizers and non-sensitizers with outstanding precision equal to or better than existing validated alternative models. Moreover, this model allows to predict sensitization potency of chemicals. The BMDC test could therefore be proposed as an additional tool to assess the sensitizing potential and potency of chemicals.
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Affiliation(s)
- Fabrice Battais
- French Research and Safety Institute for the Prevention of Occupational Accidents and Diseases (INRS), Toxicology and Biomonitoring Division, Vandoeuvre les Nancy, France
| | - Isabelle Langonné
- French Research and Safety Institute for the Prevention of Occupational Accidents and Diseases (INRS), Toxicology and Biomonitoring Division, Vandoeuvre les Nancy, France
| | - Samuel Muller
- French Research and Safety Institute for the Prevention of Occupational Accidents and Diseases (INRS), Toxicology and Biomonitoring Division, Vandoeuvre les Nancy, France
| | - Julianne Mathiot
- French Research and Safety Institute for the Prevention of Occupational Accidents and Diseases (INRS), Toxicology and Biomonitoring Division, Vandoeuvre les Nancy, France
| | - Amélie Coiscaud
- French Research and Safety Institute for the Prevention of Occupational Accidents and Diseases (INRS), Toxicology and Biomonitoring Division, Vandoeuvre les Nancy, France
| | - Adrien Audry
- French Research and Safety Institute for the Prevention of Occupational Accidents and Diseases (INRS), Toxicology and Biomonitoring Division, Vandoeuvre les Nancy, France
| | - Aurélie Martin Remy
- French Research and Safety Institute for the Prevention of Occupational Accidents and Diseases (INRS), Toxicology and Biomonitoring Division, Vandoeuvre les Nancy, France
| | - Isabelle Sponne
- French Research and Safety Institute for the Prevention of Occupational Accidents and Diseases (INRS), Toxicology and Biomonitoring Division, Vandoeuvre les Nancy, France
| | - Mélanie Mourot-Bousquenaud
- French Research and Safety Institute for the Prevention of Occupational Accidents and Diseases (INRS), Toxicology and Biomonitoring Division, Vandoeuvre les Nancy, France
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Truong DJJ, Geilenkeuser J, Wendel SV, Wilming JCH, Armbrust N, Binder EMH, Santl TH, Siebenhaar A, Gruber C, Phlairaharn T, Živanić M, Westmeyer GG. Exonuclease-enhanced prime editors. Nat Methods 2024; 21:455-464. [PMID: 38302659 PMCID: PMC10927552 DOI: 10.1038/s41592-023-02162-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 12/19/2023] [Indexed: 02/03/2024]
Abstract
Prime editing (PE) is a powerful gene-editing technique based on targeted gRNA-templated reverse transcription and integration of the de novo synthesized single-stranded DNA. To circumvent one of the main bottlenecks of the method, the competition of the reverse-transcribed 3' flap with the original 5' flap DNA, we generated an enhanced fluorescence-activated cell sorting reporter cell line to develop an exonuclease-enhanced PE strategy ('Exo-PE') composed of an improved PE complex and an aptamer-recruited DNA-exonuclease to remove the 5' original DNA flap. Exo-PE achieved better overall editing efficacy than the reference PE2 strategy for insertions ≥30 base pairs in several endogenous loci and cell lines while maintaining the high editing precision of PE2. By enabling the precise incorporation of larger insertions, Exo-PE complements the growing palette of different PE tools and spurs additional refinements of the PE machinery.
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Affiliation(s)
- Dong-Jiunn Jeffery Truong
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
- Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine,Technical University of Munich, Munich, Germany
| | - Julian Geilenkeuser
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
- Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine,Technical University of Munich, Munich, Germany
| | - Stephanie Victoria Wendel
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
- Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine,Technical University of Munich, Munich, Germany
| | - Julius Clemens Heinrich Wilming
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
- Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine,Technical University of Munich, Munich, Germany
| | - Niklas Armbrust
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
- Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine,Technical University of Munich, Munich, Germany
| | - Eva Maria Hildegard Binder
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
- Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine,Technical University of Munich, Munich, Germany
| | - Tobias Heinrich Santl
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
- Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine,Technical University of Munich, Munich, Germany
| | - Annika Siebenhaar
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
- Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine,Technical University of Munich, Munich, Germany
| | - Christoph Gruber
- Institute of Developmental Genetics, Helmholtz Munich, Neuherberg, Germany
| | - Teeradon Phlairaharn
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
- Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine,Technical University of Munich, Munich, Germany
| | - Milica Živanić
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany
- Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine,Technical University of Munich, Munich, Germany
| | - Gil Gregor Westmeyer
- Institute for Synthetic Biomedicine, Helmholtz Munich, Neuherberg, Germany.
- Department of Bioscience, TUM School of Natural Sciences and TUM School of Medicine,Technical University of Munich, Munich, Germany.
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Brooks HL, de Castro Brás LE, Brunt KR, Sylvester MA, Parvatiyar MS, Sirish P, Bansal SS, Sule R, Eadie AL, Knepper MA, Fenton RA, Lindsey ML, DeLeon-Pennell KY, Gomes AV. Guidelines on antibody use in physiology research. Am J Physiol Renal Physiol 2024; 326:F511-F533. [PMID: 38234298 DOI: 10.1152/ajprenal.00347.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/08/2024] [Accepted: 01/08/2024] [Indexed: 01/19/2024] Open
Abstract
Antibodies are one of the most used reagents in scientific laboratories and are critical components for a multitude of experiments in physiology research. Over the past decade, concerns about many biological methods, including those that use antibodies, have arisen as several laboratories were unable to reproduce the scientific data obtained in other laboratories. The lack of reproducibility could be largely attributed to inadequate reporting of detailed methods, no or limited verification by authors, and the production and use of unvalidated antibodies. The goal of this guideline article is to review best practices concerning commonly used techniques involving antibodies, including immunoblotting, immunohistochemistry, and flow cytometry. Awareness and integration of best practices will increase the rigor and reproducibility of these techniques and elevate the quality of physiology research.
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Affiliation(s)
- Heddwen L Brooks
- Department of Physiology, Tulane University School of Medicine, New Orleans, Louisiana, United States
| | | | - Keith R Brunt
- Department of Pharmacology, Faculty of Medicine, Dalhousie University, Saint John, New Brunswick, Canada
| | - Megan A Sylvester
- Department of Physiology, College of Medicine, University of Arizona, Tucson, Arizona, United States
| | - Michelle S Parvatiyar
- Department of Nutrition and Integrative Physiology, Florida State University, Tallahassee, Florida, United States
| | - Padmini Sirish
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of California, Davis, California, United States
| | - Shyam S Bansal
- Department of Cellular and Molecular Physiology, Heart and Vascular Institute, Pennsylvania State University Hershey Medical Center, Hershey, Pennsylvania, United States
| | - Rasheed Sule
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, California, United States
| | - Ashley L Eadie
- Department of Pharmacology, Faculty of Medicine, Dalhousie University, Saint John, New Brunswick, Canada
| | - Mark A Knepper
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Robert A Fenton
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Merry L Lindsey
- School of Graduate Studies, Meharry Medical College, Nashville, Tennessee, United States
- Research Service, Nashville Veterans Affairs Medical Center, Nashville, Tennessee, United States
| | - Kristine Y DeLeon-Pennell
- Division of Cardiology, Department of Medicine, School of Medicine, Medical University of South Carolina, Charleston, South Carolina, United States
- Research Service, Ralph H Johnson Veterans Affairs Medical Center, Charleston, South Carolina, United States
| | - Aldrin V Gomes
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, California, United States
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42
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Heng E, Neuwirth M, Mas F, Contant G, Mazighi M, Feriel J, Montpellier B, Brumpt C, Jourdi G, Curis E, Siguret V. Assessment of inter-operator variability in peripheral monocyte subset gating strategy using flow cytometry in patients with suspected acute stroke. Cytometry A 2024; 105:171-180. [PMID: 37971361 DOI: 10.1002/cyto.a.24810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/09/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Innovative tools to reliably identify patients with acute stroke are needed. Peripheral monocyte subsets, that is, classical-Mon1, intermediate-Mon2, and non-classical-Mon3, with their activation marker expression analyzed using flow-cytometry (FCM) could be interesting cell biomarker candidates. AIM To assess the inter-operator variability in a new peripheral monocyte subset gating strategy using FCM in patients with suspected acute stroke. METHODS In BOOST-study ("Biomarkers-algOrithm-for-strOke-diagnoSis-and Treatment-resistance-prediction," NCT04726839), patients ≥18 years with symptoms suggesting acute stroke within the last 24 h were included. Blood was collected upon admission to emergency unit. FCM analysis was performed using the FACS-CANTO-II® flow-cytometer and Flow-Jo™-software. Analyzed markers were CD45/CD91/CD14/CD16 (monocyte backbone) and CD62L/CD11b/HLA-DR/CD86/CCR2/ICAM-1/CX3CR1/TF (activation markers). Inter-operator agreement (starting from raw-data files) was quantified by the measure distribution and, for each patient, the coefficient of variation (CV). RESULTS Three operators analyzed 20 patient blood samples. Median inter-operator CVs were below the pre-specified tolerance limits (10% [for Mon1 counts], 20% [Mon2, Mon3 counts], 15% [activation marker median-fluorescence-intensities]). We observed a slight, but systematic, inter-operator effect. Overall, absolute inter-operator differences in fractions of monocyte subsets were <0.03. CONCLUSION Our gating strategy allowed monocyte subset gating with an acceptable inter-operator variability. Although low, the inter-operator effect should be considered in monocyte data analysis of BOOST-patients.
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Affiliation(s)
- Evelyne Heng
- INSERM, Innovative Therapies in Haemostasis, Université Paris Cité, Paris, France
- Service d'Hématologie Biologique, Hôpital Lariboisière, APHP.Nord, Paris, France
| | - Marie Neuwirth
- INSERM, Innovative Therapies in Haemostasis, Université Paris Cité, Paris, France
- Service d'Hématologie Biologique, Hôpital Lariboisière, APHP.Nord, Paris, France
| | - Floriane Mas
- R&D Hematology and Hemostasis department, Biocytex, Marseille, France
| | | | - Mikaël Mazighi
- Unité Neuro-vasculaire, Hôpital Lariboisière, APHP.Nord, Paris, France
| | - Joffrey Feriel
- Développement clinique, Diagnostica Stago, Asnières-sur-Seine, France
| | | | - Caren Brumpt
- Service d'Hématologie Biologique, Hôpital Lariboisière, APHP.Nord, Paris, France
| | - Georges Jourdi
- INSERM, Innovative Therapies in Haemostasis, Université Paris Cité, Paris, France
- Service d'Hématologie Biologique, Hôpital Lariboisière, APHP.Nord, Paris, France
| | - Emmanuel Curis
- Service d'Hématologie Biologique, Hôpital Lariboisière, APHP.Nord, Paris, France
- UR 7537 BioSTM (Biostatistics), Faculté de Pharmacie de Paris, Université Paris Cité, Paris, France
| | - Virginie Siguret
- INSERM, Innovative Therapies in Haemostasis, Université Paris Cité, Paris, France
- Service d'Hématologie Biologique, Hôpital Lariboisière, APHP.Nord, Paris, France
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43
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Almuwaqqat Z, Wittbrodt M, Moazzami K, Garcia M, Lima B, Martini A, Sullivan S, Nye JA, Pearce BD, Shah AJ, Waller EK, Vaccarino V, Bremner JD, Quyyumi AA. Acute psychological stress-induced progenitor cell mobilization and cardiovascular events. J Psychosom Res 2024; 178:111412. [PMID: 38281471 PMCID: PMC10823179 DOI: 10.1016/j.jpsychores.2023.111412] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 05/29/2023] [Accepted: 06/12/2023] [Indexed: 01/30/2024]
Abstract
OBJECTIVE Certain brain activation responses to psychological stress are associated with worse outcomes in CVD patients. We hypothesized that elevated acute psychological stress, manifesting as greater activity within neural centers for emotional regulation, mobilizes CPC from the bone marrow to the peripheral blood and predicts future cardiovascular events. METHODS In 427 patients with stable CAD undergoing a laboratory-based mental stress (MS) test, CPCs were enumerated using flow cytometry as CD34-expressing mononuclear cells (CD34+) before and 45 min after stress. Changes in brain regional blood flow with MS were measured using high resolution-positron emission tomography (HR-PET). Association between the change in CPC with MS and the risk of cardiovascular death or myocardial infarction (MI) during a 5-year follow-up period was analyzed. RESULTS MS increased CPC counts by a mean of 150 [630] cells/mL (15%), P < 0.001. Greater limbic lobe activity, indicative of activation of emotion-regulating centers, was associated with greater CPC mobilization (P < 0.005). Using Fine and Gray models after adjustment for demographioc, clinical risk factors and medications use, greater CPC mobilization was associated with a higher adjusted risk of adverse events; a rise of 1000 cells/mL was associated with a 50% higher risk of cardiovascular death/MI [hazards ratio, 1.5, 95% confidence interval, 1.1-2.2). CONCLUSION Greater limbic lobe activity, brain areas involved in emotional regulation, is associated with MS-induced CPC mobilization. This mobilization isindependently associated with cardiovascular events. These findings provide novel insights into mechanisms through which psychological stressors modulate cardiovascular risk.
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Affiliation(s)
- Zakaria Almuwaqqat
- Department of Medicine, Division of Cardiology, Emory University School of Medicine, Atlanta, GA, USA; Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Matthew Wittbrodt
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, USA
| | - Kasra Moazzami
- Department of Medicine, Division of Cardiology, Emory University School of Medicine, Atlanta, GA, USA; Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Mariana Garcia
- Department of Medicine, Division of Cardiology, Emory University School of Medicine, Atlanta, GA, USA; Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Bruno Lima
- Department of Medicine, Division of Cardiology, Emory University School of Medicine, Atlanta, GA, USA
| | - Afif Martini
- Department of Medicine, Division of Cardiology, Emory University School of Medicine, Atlanta, GA, USA
| | - Samaah Sullivan
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center-Houston, Houston, Texas
| | - Jonathon A Nye
- Department of Radiology and Imaging Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Bradley D Pearce
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Amit J Shah
- Department of Medicine, Division of Cardiology, Emory University School of Medicine, Atlanta, GA, USA; Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA; Atlanta VA Medical Center, Decatur, GA, USA
| | - Edmund K Waller
- Department of Hematology and Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, USA
| | - Viola Vaccarino
- Department of Medicine, Division of Cardiology, Emory University School of Medicine, Atlanta, GA, USA; Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - J Douglas Bremner
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, USA; Atlanta VA Medical Center, Decatur, GA, USA; Department of Radiology and Imaging Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Arshed A Quyyumi
- Department of Medicine, Division of Cardiology, Emory University School of Medicine, Atlanta, GA, USA.
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44
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Pang K, Liu Q, Zhu Y, Wei X. In vivo photoacoustic flow cytometry-based study of the effect of melanin content on melanoma metastasis. J Biophotonics 2024; 17:e202300405. [PMID: 38010214 DOI: 10.1002/jbio.202300405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 11/29/2023]
Abstract
A major cause of death in cancer patients is distant metastasis of tumors, in which circulating tumor cells (CTCs) are an important marker. Photoacoustic flow cytometry (PAFC) can monitor CTCs in real time, non-invasively, and label-free; we built a PAFC system and validated the feasibility of PAFC for monitoring CTCs using in vivo animal experiments. By cultivating heavily-pigmented and moderately-pigmented melanoma cells, more CTCs were detected in mice inoculated with moderately-pigmented tumor cells, resulting in more distant metastases and poorer survival status. Tumor cells with lower melanin content may produce more CTCs, increasing the risk of metastasis. CTC melanin content may be down-regulated during the metastatic which may be a potential indicator for assessing the risk of melanoma metastasis. In conclusion, PAFC can be used to assess the risk of melanoma metastasis by dynamically monitoring the number of CTCs and the CTC melanin content in future clinical diagnoses.
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Affiliation(s)
- Kai Pang
- School of Instrument Science and Opto Electronics Engineering of Beijing Information Science & Technology University, Beijing, China
| | - Qi Liu
- Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yuxi Zhu
- School of Instrument Science and Opto Electronics Engineering of Beijing Information Science & Technology University, Beijing, China
| | - Xunbin Wei
- Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute and Biomedical Engineering Department, Peking University, Beijing, China
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45
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Rulmont J, Tassin F, Keutgens A. [Is hematological cytology outdated at the age of molecular biology and flow cytometry ? Report of a VEXAS syndrome clinical case]. Rev Med Liege 2024; 79:137-142. [PMID: 38487906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
VEXAS syndrome is a new entity, described as the first one of a new class of hemato-inflammatory diseases. Through this article and based on the first case highlighted at the CHU of Liege, we offer you a review of the literature as well as an overview of different laboratory techniques used for the diagnosis of this syndrome.
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Affiliation(s)
| | - Françoise Tassin
- Service d'Hématologie biologique et Immuno-Hématologie, CHU Liège, Belgique
| | - Aurore Keutgens
- Service d'Hématologie biologique et Immuno-Hématologie, CHU Liège, Belgique
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46
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Wang L, Cao C, Qiu J, Zhang J, He Q, Song L, Xie L, Ma J. Correlation between PD-1 and sPD-L1 expression levels in peripheral blood of DLBCL patients and their clinicopathological characteristics. Cell Mol Biol (Noisy-le-grand) 2024; 70:44-50. [PMID: 38430041 DOI: 10.14715/cmb/2024.70.2.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Indexed: 03/03/2024]
Abstract
Molecular pathology and clinical characteristics play a crucial role in guiding treatment selection and predicting the prognosis of diffuse large B-cell lymphoma (DLBCL). The programmed cell death protein 1 (PD-1) and its ligand (PD-L1), have emerged as pivotal regulators of immune checkpoints in cancer. The objectives of this study are to investigate the correlation between the expression levels of PD-1 and soluble PD-L1 (sPD-L1) in the peripheral blood of DLBCL patients, analyze their clinicopathological characteristics, and identify the optimal beneficiary group for PD-1/PD-L1 blockade. Peripheral blood samples were collected from 36 DLBCL patients before their initial treatment at Shandong Cancer Hospital between December 2018 and July 2019. The expression levels of PD-1 and sPD-L1 were measured using flow cytometry and enzyme-linked immunosorbent assay (ELISA), respectively. The clinicopathological characteristics, including age, sex, Ann Arbor stage, International Prognostic Index (IPI) score, response to treatment, etc., were recorded for each patient. The surface expression of PD-1 on peripheral blood T cells was significantly higher in DLBCL patients compared to healthy controls. There was a significant association between elevated PD-1 expression levels and the advanced Ann Arbor stage (P=0.0153) as well as the B group (P=0.0184). Higher sPD-L1 levels were associated with the GCB subtype according to Hans's classification (P=0.0435). The expression levels of PD-1 and sPD-L1 in the peripheral blood of DLBCL patients are significantly correlated with advanced disease stage, B group, and GCB subtype according to Hans's classification. This suggests that the PD-1/PD-L1 axis play a critical role in specific subgroups of DLBCL. Targeting this axis could serve as a potential therapeutic strategy to enhance the clinical outcomes of DLBCL patients. Further studies are necessary to explore the prognostic implications of PD-1 and sPD-L1 expression levels in DLBCL patients.
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Affiliation(s)
- Liang Wang
- Department of Hematology, Shengli Oilfield Central Hospital, Dongying 257097, China.
| | - Congcong Cao
- Department of Hematology, the People's Hospital of Pingyi County, Linyi 273300, China.
| | - Juan Qiu
- Department of Hematology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China.
| | - Jianing Zhang
- Department of Hematology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China.
| | - Qiang He
- Department of Hematology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China.
| | - Lihua Song
- Department of Hematology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China.
| | - Linna Xie
- Department of Hematology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China.
| | - Ji Ma
- Department of Hematology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China.
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Zhang X, Wei X, Wu CX, Men X, Wang J, Bai JJ, Sun XY, Wang Y, Yang T, Lim CT, Chen ML, Wang JH. Multiplex Profiling of Biomarker and Drug Uptake in Single Cells Using Microfluidic Flow Cytometry and Mass Spectrometry. ACS Nano 2024; 18:6612-6622. [PMID: 38359901 PMCID: PMC10906074 DOI: 10.1021/acsnano.3c12803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/17/2024]
Abstract
To perform multiplex profiling of single cells and eliminate the risk of potential sample loss caused by centrifugation, we developed a microfluidic flow cytometry and mass spectrometry system (μCytoMS) to evaluate the drug uptake and induced protein expression at the single cell level. It involves a microfluidic chip for the alignment and purification of single cells followed by detection with laser-induced fluorescence (LIF) and inductively coupled plasma mass spectrometry (ICP-MS). Biofunctionalized nanoprobes (BioNPs), conjugating ∼3000 6-FAM-Sgc8 aptamers on a single gold nanoparticle (AuNP) (Kd = 0.23 nM), were engineered to selectively bind with protein tyrosine kinase 7 (PTK7) on target cells. PTK7 expression induced by oxaliplatin (OXA) uptake was assayed with LIF, while ICP-MS measurement of 195Pt revealed OXA uptake of the drug in individual cells, which provided further in-depth information about the drug in relation to PTK7 expression. At an ultralow flow of ∼0.043 dyn/cm2 (20 μL/min), the chip facilitates the extremely fast focusing of BioNPs labeled single cells without the need for centrifugal purification. It ensures multiplex profiling of single cells at a throughput speed of 500 cells/min as compared to 40 cells/min in previous studies. Using a machine learning algorithm to initially profile drug uptake and marker expression in tumor cell lines, μCytoMS was able to perform in situ profiling of the PTK7 response to the OXA at single-cell resolution for tests done on clinical samples from 10 breast cancer patients. It offers great potential for multiplex single-cell phenotypic analysis and clinical diagnosis.
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Affiliation(s)
- Xuan Zhang
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
- Institute
for Health Innovation and Technology, National
University of Singapore, 117599, Singapore
- Academy
of Medical Science, Shanxi Medical University, Taiyuan 030001, China
| | - Xing Wei
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Cheng-Xin Wu
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Xue Men
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Jiao Wang
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Jun-Jie Bai
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Xiao-Yan Sun
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Yu Wang
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Ting Yang
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Chwee Teck Lim
- Institute
for Health Innovation and Technology, National
University of Singapore, 117599, Singapore
- Department
of Biomedical Engineering, National University
of Singapore, 117576, Singapore
| | - Ming-Li Chen
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Jian-Hua Wang
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
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48
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Oyaert M, De Bruyne S, Van Camp C, Van de Caveye I, Delanghe J. Lipid droplets may interfere with urinary red blood cell and crystal counts by urinary flow cytometry. Clin Chem Lab Med 2024; 62:e65-e67. [PMID: 37650386 DOI: 10.1515/cclm-2023-0783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 08/20/2023] [Indexed: 09/01/2023]
Affiliation(s)
- Matthijs Oyaert
- Department of Laboratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Sander De Bruyne
- Department of Laboratory Medicine, Ghent University Hospital, Ghent, Belgium
| | | | | | - Joris Delanghe
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
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49
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Kapanadze T, Gamrekelashvili J, Sablotny S, Schroth FN, Xu Y, Chen R, Rong S, Shushakova N, Gueler F, Haller H, Limbourg FP. Validation of CSF-1 receptor (CD115) staining for analysis of murine monocytes by flow cytometry. J Leukoc Biol 2024; 115:573-582. [PMID: 38038378 DOI: 10.1093/jleuko/qiad147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 10/18/2023] [Accepted: 11/09/2023] [Indexed: 12/02/2023] Open
Abstract
CD115, the receptor for colony stimulating factor 1, is essential for survival and differentiation of monocytes and macrophages and is therefore frequently used to define monocyte subsets and their progenitors in immunological assays. However, CD115 surface expression and detection by flow cytometry is greatly influenced by cell isolation and processing methods, organ source, and disease context. In a systematic analysis of murine monocytes, we define experimental conditions that preserve or limit CD115 surface expression and staining by flow cytometry. We also find that, independent of conditions, CD115 surface levels are consistently lower in Ly6Clo monocytes than in Ly6Chi monocytes, with the exception of Ly6Clo monocytes in the bone marrow. Furthermore, in contrast to IL-34, the presence of colony stimulating factor 1 impairs CD115 antibody staining in a dose-dependent manner, which, in a model of ischemic kidney injury with elevated levels of colony stimulating factor 1, influenced quantification of kidney monocytes. Thus, staining and experimental conditions affect quantitative and qualitative analysis of monocytes and may influence experimental conclusions.
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Affiliation(s)
- Tamar Kapanadze
- Vascular Medicine Research, Department of Nephrology and Hypertension, Hannover Medical School, Hannover, D 30625, Germany
- Department of Nephrology and Hypertension, Hannover Medical School, Hannover D 30625, Germany
| | - Jaba Gamrekelashvili
- Vascular Medicine Research, Department of Nephrology and Hypertension, Hannover Medical School, Hannover, D 30625, Germany
- Department of Nephrology and Hypertension, Hannover Medical School, Hannover D 30625, Germany
| | - Stefan Sablotny
- Vascular Medicine Research, Department of Nephrology and Hypertension, Hannover Medical School, Hannover, D 30625, Germany
- Department of Nephrology and Hypertension, Hannover Medical School, Hannover D 30625, Germany
| | - Frauline Nicole Schroth
- Vascular Medicine Research, Department of Nephrology and Hypertension, Hannover Medical School, Hannover, D 30625, Germany
- Department of Nephrology and Hypertension, Hannover Medical School, Hannover D 30625, Germany
| | - Yuangao Xu
- Vascular Medicine Research, Department of Nephrology and Hypertension, Hannover Medical School, Hannover, D 30625, Germany
- Department of Nephrology and Hypertension, Hannover Medical School, Hannover D 30625, Germany
| | - Rongjun Chen
- Department of Nephrology and Hypertension, Hannover Medical School, Hannover D 30625, Germany
| | - Song Rong
- Department of Nephrology and Hypertension, Hannover Medical School, Hannover D 30625, Germany
| | - Nelli Shushakova
- Department of Nephrology and Hypertension, Hannover Medical School, Hannover D 30625, Germany
- Phenos GmbH, Hannover, Germany
| | - Faikah Gueler
- Department of Nephrology and Hypertension, Hannover Medical School, Hannover D 30625, Germany
| | - Hermann Haller
- Department of Nephrology and Hypertension, Hannover Medical School, Hannover D 30625, Germany
| | - Florian P Limbourg
- Vascular Medicine Research, Department of Nephrology and Hypertension, Hannover Medical School, Hannover, D 30625, Germany
- Department of Nephrology and Hypertension, Hannover Medical School, Hannover D 30625, Germany
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50
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Ciaparrone G, Pirone D, Fiore P, Xin L, Xiao W, Li X, Bardozzo F, Bianco V, Miccio L, Pan F, Memmolo P, Tagliaferri R, Ferraro P. Label-free cell classification in holographic flow cytometry through an unbiased learning strategy. Lab Chip 2024; 24:924-932. [PMID: 38264771 DOI: 10.1039/d3lc00385j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Nowadays, label-free imaging flow cytometry at the single-cell level is considered the stepforward lab-on-a-chip technology to address challenges in clinical diagnostics, biology, life sciences and healthcare. In this framework, digital holography in microscopy promises to be a powerful imaging modality thanks to its multi-refocusing and label-free quantitative phase imaging capabilities, along with the encoding of the highest information content within the imaged samples. Moreover, the recent achievements of new data analysis tools for cell classification based on deep/machine learning, combined with holographic imaging, are urging these systems toward the effective implementation of point of care devices. However, the generalization capabilities of learning-based models may be limited from biases caused by data obtained from other holographic imaging settings and/or different processing approaches. In this paper, we propose a combination of a Mask R-CNN to detect the cells, a convolutional auto-encoder, used to the image feature extraction and operating on unlabelled data, thus overcoming the bias due to data coming from different experimental settings, and a feedforward neural network for single cell classification, that operates on the above extracted features. We demonstrate the proposed approach in the challenging classification task related to the identification of drug-resistant endometrial cancer cells.
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Affiliation(s)
- Gioele Ciaparrone
- Neurone Lab, Department of Management and Innovation Systems (DISA-MIS), University of Salerno, Fisciano, Italy.
| | - Daniele Pirone
- CNR - Institute of Applied Sciences and Intelligent Systems "Eduardo Caianiello", Pozzuoli, Italy.
| | - Pierpaolo Fiore
- Neurone Lab, Department of Management and Innovation Systems (DISA-MIS), University of Salerno, Fisciano, Italy.
| | - Lu Xin
- Key Laboratory of Precision Opto-Mechatronics Technology of Ministry of Education, School of Instrumentation Science & Optoelectronics Engineering, Beihang University, 100191 Beijing, China.
| | - Wen Xiao
- Key Laboratory of Precision Opto-Mechatronics Technology of Ministry of Education, School of Instrumentation Science & Optoelectronics Engineering, Beihang University, 100191 Beijing, China.
| | - Xiaoping Li
- Department of Obstetrics and Gynecology, Peking University People's Hospital, Beijing 100044, China
| | - Francesco Bardozzo
- Neurone Lab, Department of Management and Innovation Systems (DISA-MIS), University of Salerno, Fisciano, Italy.
- CNR - Institute of Applied Sciences and Intelligent Systems "Eduardo Caianiello", Pozzuoli, Italy.
| | - Vittorio Bianco
- CNR - Institute of Applied Sciences and Intelligent Systems "Eduardo Caianiello", Pozzuoli, Italy.
| | - Lisa Miccio
- CNR - Institute of Applied Sciences and Intelligent Systems "Eduardo Caianiello", Pozzuoli, Italy.
| | - Feng Pan
- Key Laboratory of Precision Opto-Mechatronics Technology of Ministry of Education, School of Instrumentation Science & Optoelectronics Engineering, Beihang University, 100191 Beijing, China.
| | - Pasquale Memmolo
- CNR - Institute of Applied Sciences and Intelligent Systems "Eduardo Caianiello", Pozzuoli, Italy.
| | - Roberto Tagliaferri
- Neurone Lab, Department of Management and Innovation Systems (DISA-MIS), University of Salerno, Fisciano, Italy.
- CNR - Institute of Applied Sciences and Intelligent Systems "Eduardo Caianiello", Pozzuoli, Italy.
| | - Pietro Ferraro
- CNR - Institute of Applied Sciences and Intelligent Systems "Eduardo Caianiello", Pozzuoli, Italy.
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